Performance Decline

kw24 · August 26, 2020, 5:31pm

GROMACS version: 2020.3
GROMACS modification: No

Hi everyone,

I’ve just been going through the tutorials for a few days, but I’ve noticed a recent decline in performance from ~20 ns/day to ~8 ns/day or even lower at times. This all started with Tutorial 3 for umbrella sampling. I thought that it could’ve been because of the extra toll from more atoms, but Tutorial 1 had a few hundred more and performed significantly better.

Why is my performance getting worse and how can I fix it? I’m completely new to computational methods, so I’d be grateful for any help!

I’m using a Mac desktop with these specifications:
Processor - 2.7 GHz Quad-Core Intel Core i5
GPU - Intel Iris Pro 1536 MB

Thank you!

Masrul · August 26, 2020, 10:29pm

If your CPUs do other jobs besides gromacs (e.g.: web browser, other softwares) in a personal computer, then resources are shared. If this is a case, apparently performance will decrease. Thread pinning can be an option (mdrun -pin on).

kw24 · August 26, 2020, 11:01pm

That’s good to know, but I’ve just been leaving my computer unattended with any mostly all unnecessary programs closed. I’ll try the thread pinning though, thanks!

pszilard · August 27, 2020, 11:27am

Compare your log files, in particular the performance report at the end which should be able to allow you to compare the two runs and give you an idea whether all parts of the run are slower in one case or perhaps some additional computation you enabled in latter runs adds extra work making the overall performance lower.

kw24 · August 27, 2020, 6:27pm

I’ll attach 2 npt.log excerpts here. I don’t really see any extra computations, but I’m not really familiar with the content.

Faster run:

> 	M E G A - F L O P S   A C C O U N T I N G
> 
>  NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
>  RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
>  W3=SPC/TIP3p  W4=TIP4p (single or pairs)
>  V&F=Potential and force  V=Potential only  F=Force only
> 
>  Computing:                               M-Number         M-Flops  % Flops
> -----------------------------------------------------------------------------
>  Pair Search distance check           15120.751268      136086.761     0.2
>  NxN Ewald Elec. + LJ [F]            534341.294592    35266525.443    52.2
>  NxN Ewald Elec. + LJ [V&F]            5407.896848      578644.963     0.9
>  NxN Ewald Elec. [F]                 470672.551296    28711025.629    42.5
>  NxN Ewald Elec. [V&F]                 4764.276400      400199.218     0.6
>  1,4 nonbonded interactions             255.305106       22977.460     0.0
>  Calc Weights                          5081.501628      182934.059     0.3
>  Spread Q Bspline                    108405.368064      216810.736     0.3
>  Gather F Bspline                    108405.368064      650432.208     1.0
>  3D-FFT                              139519.590336     1116156.723     1.7
>  Solve PME                               96.801936        6195.324     0.0
>  Shift-X                                 33.909876         203.459     0.0
>  Bonds                                   51.251025        3023.810     0.0
>  Angles                                 177.353547       29795.396     0.0
>  Propers                                 21.300426        4877.798     0.0
>  RB-Dihedrals                           197.503950       48783.476     0.1
>  Pos. Restr.                             50.051001        2502.550     0.0
>  Virial                                 169.638921        3053.501     0.0
>  Stop-CM                                 16.971876         169.719     0.0
>  Calc-Ekin                              338.827752        9148.349     0.0
>  Lincs                                   47.950959        2877.058     0.0
>  Lincs-Mat                              238.804776         955.219     0.0
>  Constraint-V                          1691.333826       13530.671     0.0
>  Constraint-Vir                         164.367867        3944.829     0.0
>  Settle                                 531.810636      171774.835     0.3
> -----------------------------------------------------------------------------
>  Total                                                67582629.192   100.0
> -----------------------------------------------------------------------------
> 
> 
>      R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
> 
> On 1 MPI rank, each using 4 OpenMP threads
> 
>  Computing:          Num   Num      Call    Wall time         Giga-Cycles
>                      Ranks Threads  Count      (s)         total sum    %
> -----------------------------------------------------------------------------
>  Neighbor search        1    4       1001      12.616        135.936   2.6
>  Force                  1    4      50001     381.839       4114.443  79.3
>  PME mesh               1    4      50001      69.887        753.059  14.5
>  NB X/F buffer ops.     1    4      99001       4.934         53.164   1.0
>  Write traj.            1    4        101       1.946         20.965   0.4
>  Update                 1    4      50001       2.865         30.867   0.6
>  Constraints            1    4      50001       5.418         58.381   1.1
>  Rest                                           1.800         19.396   0.4
> -----------------------------------------------------------------------------
>  Total                                        481.304       5186.212 100.0
> -----------------------------------------------------------------------------
>  Breakdown of PME mesh computation
> -----------------------------------------------------------------------------
>  PME spread             1    4      50001      30.501        328.660   6.3
>  PME gather             1    4      50001      17.960        193.526   3.7
>  PME 3D-FFT             1    4     100002      19.339        208.385   4.0
>  PME solve Elec         1    4      50001       1.981         21.350   0.4
> -----------------------------------------------------------------------------
> 
>                Core t (s)   Wall t (s)        (%)
>        Time:     1924.993      481.304      400.0
>                  (ns/day)    (hour/ns)
> Performance:       17.952        1.337
> Finished mdrun on rank 0 Fri Aug 21 17:31:53 2020

Slower run:

	M E G A - F L O P S   A C C O U N T I N G

 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
 V&F=Potential and force  V=Potential only  F=Force only

 Computing:                               M-Number         M-Flops  % Flops
-----------------------------------------------------------------------------
 Pair Search distance check           12786.518692      115078.668     0.1
 NxN Ewald Elec. + LJ [F]           1068744.793248    70537156.354    52.1
 NxN Ewald Elec. + LJ [V&F]           10816.965216     1157415.278     0.9
 NxN LJ [F]                            1345.367232       44397.119     0.0
 NxN LJ [V&F]                            13.618496         585.595     0.0
 NxN Ewald Elec. [F]                 987500.292768    60237517.859    44.5
 NxN Ewald Elec. [V&F]                 9994.694176      839554.311     0.6
 1,4 nonbonded interactions              94.501890        8505.170     0.0
 Calc Weights                          4981.149621      179321.386     0.1
 Spread Q Bspline                    106264.525248      212529.050     0.2
 Gather F Bspline                    106264.525248      637587.151     0.5
 3D-FFT                              155438.308704     1243506.470     0.9
 Solve PME                               58.801176        3763.275     0.0
 Shift-X                                 16.636707          99.820     0.0
 Angles                                  82.751655       13902.278     0.0
 Propers                                 28.750575        6583.882     0.0
 Impropers                               28.000560        5824.116     0.0
 Pos. Restr.                             46.000920        2300.046     0.0
 Virial                                 332.553252        5985.959     0.0
 Stop-CM                                 16.669914         166.699     0.0
 P-Coupling                             332.103207        1992.619     0.0
 Calc-Ekin                              664.206414       17933.573     0.0
 Lincs                                   56.753405        3405.204     0.0
 Lincs-Mat                              993.059580        3972.238     0.0
 Constraint-V                          1714.818590       13718.549     0.0
 Constraint-Vir                         331.633160        7959.196     0.0
 Settle                                 533.782025      172411.594     0.1
-----------------------------------------------------------------------------
 Total                                               135473173.461   100.0
-----------------------------------------------------------------------------


     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 1 MPI rank, each using 4 OpenMP threads

 Computing:          Num   Num      Call    Wall time         Giga-Cycles
                     Ranks Threads  Count      (s)         total sum    %
-----------------------------------------------------------------------------
 Neighbor search        1    4        501      12.283        132.361   1.0
 Force                  1    4      50001    1042.037      11228.525  87.9
 PME mesh               1    4      50001      96.655       1041.511   8.2
 NB X/F buffer ops.     1    4      99501      10.030        108.075   0.8
 Write traj.            1    4         52       1.762         18.989   0.1
 Update                 1    4      50001       5.096         54.917   0.4
 Constraints            1    4      50003      13.055        140.672   1.1
 Rest                                           3.986         42.950   0.3
-----------------------------------------------------------------------------
 Total                                       1184.904      12768.001 100.0
-----------------------------------------------------------------------------
 Breakdown of PME mesh computation
-----------------------------------------------------------------------------
 PME spread             1    4      50001      42.483        457.776   3.6
 PME gather             1    4      50001      27.018        291.130   2.3
 PME 3D-FFT             1    4     100002      24.533        264.358   2.1
 PME solve Elec         1    4      50001       2.465         26.563   0.2
-----------------------------------------------------------------------------

               Core t (s)   Wall t (s)        (%)
       Time:     4739.612     1184.904      400.0
                 (ns/day)    (hour/ns)
Performance:        7.292        3.291
Finished mdrun on rank 0 Sun Aug 23 14:36:20 2020

Tell me if you notice anything.

pszilard · August 30, 2020, 4:01pm

Comparing the flops accounting what is clear is that the pair interaction work (“NXN Ewald…” entries) in one of the runs is ~2x higher (while other work that scales with the #atoms is similar) which suggests that the cutoff (or density) is likely significantly larger in one of the systems. Perhaps you’re comparing a simulation set up with the AMBER to one with CHARMM.

Please post the full log, with only parts of the log shared important information is lacking making it harder to answer questions.

kw24 · August 30, 2020, 5:20pm

Of course, here you go:

I can’t post it all at once so I’ll do them piece by piece.

Slower run

>                       :-) GROMACS - gmx mdrun, 2020.3 (-:
> 
>                             GROMACS is written by:
>      Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
>     Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
>  Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
>   Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
>   Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
>     Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
>   Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
>     Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
>     Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
>    Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
>  Christian Wennberg    Maarten Wolf      Artem Zhmurov   
>                            and the project leaders:
>         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> 
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2019, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
> 
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
> 
> GROMACS:      gmx mdrun, version 2020.3
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:  /Users/profile1/gromacs-related_work/Tutorial_3
> Process ID:   25755
> Command line:
>   gmx mdrun -deffnm npt -nt 4
> 
> GROMACS version:    2020.3
> Verified release checksum is c0599e547549c2d0ef4fc678dc5a26ad0000eab045e938fed756f9ff5b99a197
> Precision:          single
> Memory model:       64 bit
> MPI library:        thread_mpi
> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
> GPU support:        OpenCL
> SIMD instructions:  AVX2_256
> FFT library:        fftw-3.3.8-sse2
> RDTSCP usage:       enabled
> TNG support:        enabled
> Hwloc support:      disabled
> Tracing support:    disabled
> C compiler:         /usr/local/bin/icc Intel 19.1.2.20200623
> C compiler flags:   -march=core-avx2 -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG
> C++ compiler:       /usr/local/bin/icpc Intel 19.1.2.20200623
> C++ compiler flags: -march=core-avx2 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG
> OpenCL include dir: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/OpenCL.framework
> OpenCL library:     /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/OpenCL.framework
> OpenCL version:     1.2
> 
> 
> Running on 1 node with total 4 cores, 4 logical cores, 0 compatible GPUs
> Hardware detected:
>   CPU info:
>     Vendor: Intel
>     Brand:  Intel(R) Core(TM) i5-4570R CPU @ 2.70GHz
>     Family: 6   Model: 70   Stepping: 1
>     Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
>   Hardware topology: Only logical processor count
>   GPU info:
>     Number of GPUs detected: 1
>     #0: name: Iris Pro, vendor: Intel, device version: OpenCL 1.2 , stat: incompatible (please recompile with GMX_OPENCL_NB_CLUSTER_SIZE=4)
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
> Lindahl
> GROMACS: High performance molecular simulations through multi-level
> parallelism from laptops to supercomputers
> SoftwareX 1 (2015) pp. 19-25
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
> Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
> GROMACS
> In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
> Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
> GROMACS 4.5: a high-throughput and highly parallel open source molecular
> simulation toolkit
> Bioinformatics 29 (2013) pp. 845-54
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
> molecular simulation
> J. Chem. Theory Comput. 4 (2008) pp. 435-447
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
> Berendsen
> GROMACS: Fast, Flexible and Free
> J. Comp. Chem. 26 (2005) pp. 1701-1719
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> E. Lindahl and B. Hess and D. van der Spoel
> GROMACS 3.0: A package for molecular simulation and trajectory analysis
> J. Mol. Mod. 7 (2001) pp. 306-317
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> H. J. C. Berendsen, D. van der Spoel and R. van Drunen
> GROMACS: A message-passing parallel molecular dynamics implementation
> Comp. Phys. Comm. 91 (1995) pp. 43-56
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
> https://doi.org/10.5281/zenodo.3923645
> -------- -------- --- Thank You --- -------- --------
> 
> Input Parameters:
>    integrator                     = md
>    tinit                          = 0
>    dt                             = 0.002
>    nsteps                         = 50000
>    init-step                      = 0
>    simulation-part                = 1
>    comm-mode                      = Linear
>    nstcomm                        = 100
>    bd-fric                        = 0
>    ld-seed                        = -1585014542
>    emtol                          = 10
>    emstep                         = 0.01
>    niter                          = 20
>    fcstep                         = 0
>    nstcgsteep                     = 1000
>    nbfgscorr                      = 10
>    rtpi                           = 0.05
>    nstxout                        = 1000
>    nstvout                        = 1000
>    nstfout                        = 0
>    nstlog                         = 1000
>    nstcalcenergy                  = 100
>    nstenergy                      = 1000
>    nstxout-compressed             = 0
>    compressed-x-precision         = 1000
>    cutoff-scheme                  = Verlet
>    nstlist                        = 5
>    pbc                            = xyz
>    periodic-molecules             = false
>    verlet-buffer-tolerance        = 0.005
>    rlist                          = 1.4
>    coulombtype                    = PME
>    coulomb-modifier               = Potential-shift
>    rcoulomb-switch                = 0
>    rcoulomb                       = 1.4
>    epsilon-r                      = 1
>    epsilon-rf                     = inf
>    vdw-type                       = Cut-off
>    vdw-modifier                   = Potential-shift
>    rvdw-switch                    = 0
>    rvdw                           = 1.4
>    DispCorr                       = EnerPres
>    table-extension                = 1
>    fourierspacing                 = 0.16
>    fourier-nx                     = 42
>    fourier-ny                     = 28
>    fourier-nz                     = 80
>    pme-order                      = 4
>    ewald-rtol                     = 1e-05
>    ewald-rtol-lj                  = 0.001
>    lj-pme-comb-rule               = Geometric
>    ewald-geometry                 = 0
>    epsilon-surface                = 0
>    tcoupl                         = Berendsen
>    nsttcouple                     = 5
>    nh-chain-length                = 0
>    print-nose-hoover-chain-variables = false
>    pcoupl                         = Berendsen
>    pcoupltype                     = Isotropic
>    nstpcouple                     = 5
>    tau-p                          = 2
>    compressibility (3x3):
>       compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
>       compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
>       compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
>    ref-p (3x3):
>       ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
>       ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
>       ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
>    refcoord-scaling               = COM
>    posres-com (3):
>       posres-com[0]= 4.97772e-01
>       posres-com[1]= 5.08396e-01
>       posres-com[2]= 2.07225e-01
>    posres-comB (3):
>       posres-comB[0]= 4.97772e-01
>       posres-comB[1]= 5.08396e-01
>       posres-comB[2]= 2.07225e-01
>    QMMM                           = false
>    QMconstraints                  = 0
>    QMMMscheme                     = 0
>    MMChargeScaleFactor            = 1
> qm-opts:
>    ngQM                           = 0
>    constraint-algorithm           = Lincs
>    continuation                   = false
>    Shake-SOR                      = false
>    shake-tol                      = 0.0001
>    lincs-order                    = 4
>    lincs-iter                     = 1
>    lincs-warnangle                = 30
>    nwall                          = 0
>    wall-type                      = 9-3
>    wall-r-linpot                  = -1
>    wall-atomtype[0]               = -1
>    wall-atomtype[1]               = -1
>    wall-density[0]                = 0
>    wall-density[1]                = 0
>    wall-ewald-zfac                = 3
>    pull                           = false
>    awh                            = false
>    rotation                       = false
>    interactiveMD                  = false
>    disre                          = No
>    disre-weighting                = Conservative
>    disre-mixed                    = false
>    dr-fc                          = 1000
>    dr-tau                         = 0
>    nstdisreout                    = 100
>    orire-fc                       = 0
>    orire-tau                      = 0
>    nstorireout                    = 100
>    free-energy                    = no
>    cos-acceleration               = 0
>    deform (3x3):
>       deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>       deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>       deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    simulated-tempering            = false
>    swapcoords                     = no
>    userint1                       = 0
>    userint2                       = 0
>    userint3                       = 0
>    userint4                       = 0
>    userreal1                      = 0
>    userreal2                      = 0
>    userreal3                      = 0
>    userreal4                      = 0
>    applied-forces:
>      electric-field:
>        x:
>          E0                       = 0
>          omega                    = 0
>          t0                       = 0
>          sigma                    = 0
>        y:
>          E0                       = 0
>          omega                    = 0
>          t0                       = 0
>          sigma                    = 0
>        z:
>          E0                       = 0
>          omega                    = 0
>          t0                       = 0
>          sigma                    = 0
>      density-guided-simulation:
>        active                     = false
>        group                      = protein
>        similarity-measure         = inner-product
>        atom-spreading-weight      = unity
>        force-constant             = 1e+09
>        gaussian-transform-spreading-width = 0.2
>        gaussian-transform-spreading-range-in-multiples-of-width = 4
>        reference-density-filename = reference.mrc
>        nst                        = 1
>        normalize-densities        = true
>        adaptive-force-scaling     = false
>        adaptive-force-scaling-time-constant = 4
> grpopts:
>    nrdf:      2254.9     64203.1
>    ref-t:         310         310
>    tau-t:         0.1         0.1
> annealing:          No          No
> annealing-npoints:           0           0
>    acc:	           0           0           0
>    nfreeze:           N           N           N
>    energygrp-flags[  0]: 0
> 
> Changing nstlist from 5 to 100, rlist from 1.4 to 1.537
> 
> Using 1 MPI thread
> Using 4 OpenMP threads 
> 
> System total charge: 0.000
> Will do PME sum in reciprocal space for electrostatic interactions.
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
> A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
> 
> Using a Gaussian width (1/beta) of 0.448228 nm for Ewald
> Potential shift: LJ r^-12: -1.764e-02 r^-6: -1.328e-01, Ewald -7.143e-06
> Initialized non-bonded Ewald tables, spacing: 1.10e-03 size: 1270
> 
> Generated table with 1268 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1268 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1268 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
> 
> Using SIMD 4x8 nonbonded short-range kernels
> 
> Using a dual 4x8 pair-list setup updated with dynamic pruning:
>   outer list: updated every 100 steps, buffer 0.137 nm, rlist 1.537 nm
>   inner list: updated every  14 steps, buffer 0.002 nm, rlist 1.402 nm
> At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
>   outer list: updated every 100 steps, buffer 0.297 nm, rlist 1.697 nm
>   inner list: updated every  14 steps, buffer 0.058 nm, rlist 1.458 nm
> 
> Using full Lennard-Jones parameter combination matrix
> 
> Long Range LJ corr.: <C6> 3.3659e-04
> 
> Removing pbc first time
> 
> Initializing LINear Constraint Solver
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
> LINCS: A Linear Constraint Solver for molecular simulations
> J. Comp. Chem. 18 (1997) pp. 1463-1472
> -------- -------- --- Thank You --- -------- --------
> 
> The number of constraints is 1135
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> S. Miyamoto and P. A. Kollman
> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
> Water Models
> J. Comp. Chem. 13 (1992) pp. 952-962
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
> Molecular dynamics with coupling to an external bath
> J. Chem. Phys. 81 (1984) pp. 3684-3690
> -------- -------- --- Thank You --- -------- --------
> 
> There are: 33207 Atoms
> 
> Constraining the starting coordinates (step 0)
> 
> Constraining the coordinates at t0-dt (step 0)
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
>   0:  System
> RMS relative constraint deviation after constraining: 3.54e-05
> Initial temperature: 309.404 K
> 
> Started mdrun on rank 0 Sun Aug 23 14:16:36 2020
> 
>            Step           Time
>               0        0.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     7.58504e+02    7.37768e+02    2.83662e+02   -2.89671e+02    2.40511e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.47644e+04   -1.64928e+03   -6.31574e+05    2.47163e+03    1.89742e-01
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -5.30446e+05    8.55125e+04   -4.44934e+05   -4.44829e+05    3.09512e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.97938e+01   -3.59468e+03    2.49748e-05
> 
>            Step           Time
>            1000        2.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.72295e+03    6.87050e+02    5.71829e+02   -1.82206e+02    2.39793e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.13517e+04   -1.63668e+03   -5.69002e+05    1.07439e+03    7.96867e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70637e+05    8.56078e+04   -3.85029e+05   -4.44396e+05    3.09857e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.85791e+01   -7.22574e+00    1.98507e-05
> 
>            Step           Time
>            2000        4.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.73212e+03    8.11117e+02    5.78414e+02   -1.28978e+02    2.40443e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.26900e+04   -1.63295e+03   -5.71205e+05    1.09543e+03    7.51106e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71265e+05    8.56248e+04   -3.85640e+05   -4.44409e+05    3.09919e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82217e+01    1.88454e+02    2.00974e-05
> 
>            Step           Time
>            3000        6.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.63898e+03    7.63986e+02    5.62962e+02   -1.70313e+02    2.40131e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.16100e+04   -1.63237e+03   -5.70302e+05    1.00078e+03    7.60845e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71754e+05    8.57354e+04   -3.86019e+05   -4.44413e+05    3.10319e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81666e+01   -3.17223e+01    1.85860e-05
> 
>            Step           Time
>            4000        8.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.66201e+03    8.03574e+02    5.76483e+02   -2.40187e+02    2.39897e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     6.98865e+04   -1.63565e+03   -5.67528e+05    1.06195e+03    7.25281e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70698e+05    8.54621e+04   -3.85236e+05   -4.44434e+05    3.09330e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.84805e+01   -2.29677e+02    2.02162e-05
> 
>            Step           Time
>            5000       10.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.68286e+03    7.57126e+02    6.10297e+02   -2.11800e+02    2.40878e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.15666e+04   -1.63704e+03   -5.70098e+05    1.01755e+03    7.46487e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71479e+05    8.53466e+04   -3.86132e+05   -4.44444e+05    3.08912e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.86142e+01   -1.14306e+01    2.02051e-05
> 
>            Step           Time
>            6000       12.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.74128e+03    7.80860e+02    5.89562e+02   -2.06272e+02    2.39793e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.13323e+04   -1.63572e+03   -5.69431e+05    1.06449e+03    7.38186e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71047e+05    8.55383e+04   -3.85508e+05   -4.44450e+05    3.09606e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.84878e+01   -6.18519e+01    2.14641e-05
> 
>            Step           Time
>            7000       14.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.79666e+03    7.69228e+02    5.34749e+02   -1.99851e+02    2.40296e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.10913e+04   -1.63367e+03   -5.68902e+05    1.06418e+03    7.03454e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70746e+05    8.56837e+04   -3.85063e+05   -4.44482e+05    3.10132e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82904e+01   -8.01907e+01    2.10140e-05
> 
>            Step           Time
>            8000       16.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.67511e+03    7.41076e+02    5.88321e+02   -1.60083e+02    2.40608e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     6.99454e+04   -1.63175e+03   -5.67110e+05    1.02702e+03    6.97072e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70167e+05    8.53409e+04   -3.84826e+05   -4.44469e+05    3.08891e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81074e+01   -3.47741e+01    1.78473e-05
> 
>            Step           Time
>            9000       18.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.68036e+03    7.57111e+02    5.49290e+02   -1.90793e+02    2.40509e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.04322e+04   -1.63096e+03   -5.67450e+05    9.85894e+02    6.58779e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70157e+05    8.54173e+04   -3.84740e+05   -4.44484e+05    3.09168e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.80317e+01   -2.56817e+01    1.89553e-05
> 
>            Step           Time
>           10000       20.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.73596e+03    7.34004e+02    5.66911e+02   -2.00885e+02    2.39483e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.13779e+04   -1.62900e+03   -5.69630e+05    1.05966e+03    6.73956e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71363e+05    8.62869e+04   -3.85076e+05   -4.44497e+05    3.12316e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.78438e+01   -4.89887e+01    2.03687e-05
> 
>            Step           Time
>           11000       22.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.67585e+03    7.60135e+02    5.69166e+02   -1.99637e+02    2.41438e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.09402e+04   -1.63025e+03   -5.69187e+05    1.04938e+03    7.22053e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71156e+05    8.59885e+04   -3.85168e+05   -4.44503e+05    3.11235e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.79634e+01   -4.71490e+01    1.82336e-05
> 
>            Step           Time
>           12000       24.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.60410e+03    7.70621e+02    5.32681e+02   -1.78460e+02    2.41394e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.23685e+04   -1.63262e+03   -5.70619e+05    1.06004e+03    7.67771e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71187e+05    8.50966e+04   -3.86090e+05   -4.44515e+05    3.08007e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81905e+01    9.99699e+01    2.06156e-05
> 
>            Step           Time
>           13000       26.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.82343e+03    7.22677e+02    5.40404e+02   -2.17934e+02    2.40235e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.21447e+04   -1.63095e+03   -5.70877e+05    1.08597e+03    6.74213e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71711e+05    8.63278e+04   -3.85383e+05   -4.44532e+05    3.12463e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.80309e+01    5.70185e+01    1.98760e-05
> 
>            Step           Time
>           14000       28.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.60604e+03    7.21354e+02    5.63308e+02   -2.04624e+02    2.40612e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.24181e+04   -1.62989e+03   -5.70238e+05    1.05617e+03    6.90138e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70956e+05    8.54198e+04   -3.85536e+05   -4.44534e+05    3.09177e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.79289e+01    2.53356e+02    1.90198e-05
> 
>            Step           Time
>           15000       30.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.69079e+03    7.38345e+02    5.88183e+02   -1.78553e+02    2.39936e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.02465e+04   -1.63026e+03   -5.67868e+05    1.08693e+03    7.52369e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70580e+05    8.58173e+04   -3.84763e+05   -4.44562e+05    3.10616e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.79643e+01   -1.21987e+02    1.94270e-05
> 
>            Step           Time
>           16000       32.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.69095e+03    7.45625e+02    5.93506e+02   -1.39075e+02    2.40316e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.18663e+04   -1.63054e+03   -5.69375e+05    1.06056e+03    6.93005e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70463e+05    8.55202e+04   -3.84943e+05   -4.44576e+05    3.09541e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.79915e+01    1.79822e+02    1.97368e-05
> 
>            Step           Time
>           17000       34.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.65455e+03    7.58503e+02    5.36711e+02   -1.88310e+02    2.39367e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.06876e+04   -1.63032e+03   -5.68939e+05    1.02553e+03    7.06379e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71451e+05    8.56544e+04   -3.85797e+05   -4.44572e+05    3.10026e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.79706e+01   -2.33882e+02    2.33506e-05
>

kw24 · August 30, 2020, 5:23pm

Slower run cont.

>            Step           Time
>           18000       36.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.73969e+03    7.37686e+02    6.03634e+02   -2.11342e+02    2.40258e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.15349e+04   -1.62977e+03   -5.69925e+05    1.06799e+03    6.73921e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71382e+05    8.56807e+04   -3.85701e+05   -4.44588e+05    3.10121e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.79176e+01    4.51847e+00    1.86058e-05
> 
>            Step           Time
>           19000       38.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.79077e+03    8.10439e+02    5.57195e+02   -2.29513e+02    2.38940e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.07996e+04   -1.63120e+03   -5.68837e+05    1.04902e+03    6.82152e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71115e+05    8.56713e+04   -3.85443e+05   -4.44599e+05    3.10087e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.80539e+01   -1.12781e+02    2.02436e-05
> 
>            Step           Time
>           20000       40.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.55516e+03    7.63042e+02    5.47801e+02   -1.69599e+02    2.40416e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.10089e+04   -1.63081e+03   -5.69270e+05    1.04641e+03    6.41272e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71466e+05    8.59381e+04   -3.85528e+05   -4.44621e+05    3.11053e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.80173e+01    1.08535e+01    1.94304e-05
> 
>            Step           Time
>           21000       42.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.69960e+03    7.84364e+02    5.71650e+02   -1.41700e+02    2.40411e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.07584e+04   -1.62881e+03   -5.69169e+05    1.00991e+03    6.18073e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71457e+05    8.53977e+04   -3.86059e+05   -4.44623e+05    3.09097e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.78262e+01   -2.74691e+01    1.95456e-05
> 
>            Step           Time
>           22000       44.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.71348e+03    7.75279e+02    5.65616e+02   -2.13998e+02    2.40010e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.17808e+04   -1.62896e+03   -5.70306e+05    1.02443e+03    6.82537e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71606e+05    8.58285e+04   -3.85778e+05   -4.44626e+05    3.10656e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.78402e+01    2.73215e+01    1.95821e-05
> 
>            Step           Time
>           23000       46.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.80985e+03    7.59334e+02    5.30763e+02   -1.84877e+02    2.40378e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.08761e+04   -1.63164e+03   -5.68668e+05    1.05014e+03    7.38252e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70683e+05    8.58472e+04   -3.84835e+05   -4.44650e+05    3.10724e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.80964e+01   -9.55946e+01    1.99366e-05
> 
>            Step           Time
>           24000       48.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.80143e+03    7.80567e+02    5.40160e+02   -2.59453e+02    2.39769e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.06743e+04   -1.62985e+03   -5.68596e+05    1.08428e+03    7.04958e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70923e+05    8.57903e+04   -3.85133e+05   -4.44653e+05    3.10518e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.79250e+01   -2.18097e+02    2.05900e-05
> 
>            Step           Time
>           25000       50.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.67152e+03    7.71123e+02    5.83705e+02   -2.13725e+02    2.41227e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.17412e+04   -1.63010e+03   -5.69975e+05    1.02711e+03    7.07070e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71194e+05    8.57453e+04   -3.85449e+05   -4.44660e+05    3.10355e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.79487e+01   -2.29032e+01    1.99029e-05
> 
>            Step           Time
>           26000       52.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.70754e+03    7.44583e+02    5.68576e+02   -1.61761e+02    2.39590e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.14828e+04   -1.62973e+03   -5.70517e+05    9.67834e+02    7.22658e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.72156e+05    8.59597e+04   -3.86196e+05   -4.44662e+05    3.11131e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.79137e+01    3.45874e+01    1.82031e-05
> 
>            Step           Time
>           27000       54.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.78495e+03    8.01932e+02    5.20708e+02   -1.74892e+02    2.38910e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.03806e+04   -1.63081e+03   -5.67896e+05    1.06571e+03    6.23147e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70634e+05    8.55769e+04   -3.85057e+05   -4.44693e+05    3.09746e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.80170e+01   -8.32043e+01    1.98570e-05
> 
>            Step           Time
>           28000       56.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.73328e+03    7.57925e+02    5.85532e+02   -1.79661e+02    2.39772e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.13457e+04   -1.63345e+03   -5.70104e+05    1.06428e+03    6.85895e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71768e+05    8.60044e+04   -3.85763e+05   -4.44702e+05    3.11293e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82700e+01   -1.46961e+02    2.20382e-05
> 
>            Step           Time
>           29000       58.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.68733e+03    8.25616e+02    5.94159e+02   -2.05692e+02    2.40765e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.03853e+04   -1.63314e+03   -5.69004e+05    1.06756e+03    6.85981e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71521e+05    8.58341e+04   -3.85686e+05   -4.44716e+05    3.10677e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82399e+01   -3.82964e+01    1.89353e-05
> 
>            Step           Time
>           30000       60.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.63136e+03    7.99711e+02    5.91905e+02   -2.00551e+02    2.39873e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.15129e+04   -1.63456e+03   -5.69453e+05    1.04739e+03    7.37991e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70979e+05    8.60359e+04   -3.84943e+05   -4.44736e+05    3.11407e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.83761e+01    1.48940e+02    1.83553e-05
> 
>            Step           Time
>           31000       62.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.68217e+03    7.32432e+02    5.64542e+02   -1.35259e+02    2.40710e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.08972e+04   -1.63205e+03   -5.68731e+05    1.01247e+03    7.25713e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70813e+05    8.54875e+04   -3.85325e+05   -4.44745e+05    3.09422e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81354e+01   -2.18382e+01    1.90446e-05
> 
>            Step           Time
>           32000       64.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.73182e+03    7.95873e+02    5.57509e+02   -1.70568e+02    2.38660e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.21995e+04   -1.63270e+03   -5.70399e+05    1.03969e+03    7.12465e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71299e+05    8.53047e+04   -3.85995e+05   -4.44757e+05    3.08760e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81982e+01    2.10322e+02    1.76449e-05
> 
>            Step           Time
>           33000       66.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.64394e+03    7.38850e+02    5.20455e+02   -1.75262e+02    2.40910e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.05471e+04   -1.63195e+03   -5.68340e+05    1.08902e+03    7.03113e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70814e+05    8.56646e+04   -3.85149e+05   -4.44765e+05    3.10063e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81264e+01   -2.99939e+01    1.80765e-05
> 
>            Step           Time
>           34000       68.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.74289e+03    8.21049e+02    5.41204e+02   -2.38198e+02    2.39946e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.14806e+04   -1.63312e+03   -5.69800e+05    1.05138e+03    7.37214e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71302e+05    8.59626e+04   -3.85340e+05   -4.44776e+05    3.11142e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82384e+01   -6.84902e+01    2.11043e-05
> 
>            Step           Time
>           35000       70.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.73218e+03    8.01274e+02    5.48433e+02   -1.89728e+02    2.40316e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.10241e+04   -1.63263e+03   -5.68991e+05    1.10756e+03    6.74840e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70893e+05    8.54419e+04   -3.85451e+05   -4.44790e+05    3.09257e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81909e+01    5.67826e+01    1.70020e-05
> 
>            Step           Time
>           36000       72.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.79542e+03    7.65931e+02    5.81705e+02   -1.86595e+02    2.39260e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.14058e+04   -1.63304e+03   -5.70042e+05    1.10317e+03    6.96240e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71587e+05    8.56771e+04   -3.85910e+05   -4.44804e+05    3.10108e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82304e+01   -1.71534e+02    2.20773e-05
> 
>            Step           Time
>           37000       74.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.77619e+03    7.61591e+02    5.19592e+02   -2.35848e+02    2.39774e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.14245e+04   -1.63306e+03   -5.69636e+05    1.05549e+03    6.96914e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71294e+05    8.56232e+04   -3.85671e+05   -4.44812e+05    3.09913e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82321e+01   -8.18356e+01    2.33924e-05
> 
> Writing checkpoint, step 37500 at Sun Aug 23 14:31:37 2020
> 
> 
>            Step           Time
>           38000       76.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.69831e+03    7.68558e+02    5.08649e+02   -1.70006e+02    2.40353e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     6.99840e+04   -1.63384e+03   -5.66968e+05    1.06893e+03    6.96111e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70012e+05    8.50570e+04   -3.84955e+05   -4.44836e+05    3.07864e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.83069e+01   -2.11010e+02    2.03854e-05
> 
>            Step           Time
>           39000       78.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.71941e+03    7.07238e+02    5.60961e+02   -1.69128e+02    2.39953e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.15866e+04   -1.63515e+03   -5.69700e+05    1.01943e+03    6.39149e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71276e+05    8.57769e+04   -3.85499e+05   -4.44853e+05    3.10470e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.84324e+01    5.23815e+01    1.96359e-05
> 
>            Step           Time
>           40000       80.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.80573e+03    7.68151e+02    5.30836e+02   -1.65207e+02    2.39724e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.14785e+04   -1.63324e+03   -5.69465e+05    1.04996e+03    6.88282e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70970e+05    8.55467e+04   -3.85423e+05   -4.44855e+05    3.09636e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82491e+01   -5.00158e+01    2.09429e-05
> 
>            Step           Time
>           41000       82.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.74945e+03    7.45484e+02    6.16679e+02   -1.70385e+02    2.40223e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.05222e+04   -1.63351e+03   -5.68448e+05    9.71256e+02    6.70689e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70954e+05    8.54918e+04   -3.85462e+05   -4.44873e+05    3.09437e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82755e+01   -3.86348e+01    1.98731e-05
> 
>            Step           Time
>           42000       84.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.78932e+03    7.68599e+02    5.96380e+02   -2.37327e+02    2.39498e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.09201e+04   -1.63539e+03   -5.69297e+05    1.03177e+03    6.23091e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71491e+05    8.54344e+04   -3.86057e+05   -4.44884e+05    3.09230e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.84561e+01   -2.09933e+02    2.06320e-05
> 
>            Step           Time
>           43000       86.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.83795e+03    7.51620e+02    6.23655e+02   -1.80285e+02    2.39487e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.15964e+04   -1.63166e+03   -5.70439e+05    1.01133e+03    6.14721e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71866e+05    8.54564e+04   -3.86410e+05   -4.44892e+05    3.09309e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.80980e+01   -2.22703e+01    2.20068e-05
> 
>            Step           Time
>           44000       88.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.76553e+03    7.46497e+02    5.36747e+02   -1.55226e+02    2.39908e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.07676e+04   -1.63227e+03   -5.69483e+05    1.04684e+03    7.67826e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71648e+05    8.57903e+04   -3.85858e+05   -4.44907e+05    3.10518e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81568e+01   -8.75074e+01    1.92759e-05
> 
>            Step           Time
>           45000       90.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.60821e+03    7.29569e+02    5.27357e+02   -1.59905e+02    2.40740e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.03465e+04   -1.63176e+03   -5.68092e+05    1.03405e+03    6.86701e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70877e+05    8.58483e+04   -3.85029e+05   -4.44921e+05    3.10728e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81082e+01   -1.58618e+02    1.97586e-05
> 
>            Step           Time
>           46000       92.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.76695e+03    7.55530e+02    5.56541e+02   -2.07205e+02    2.39672e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.21499e+04   -1.63154e+03   -5.70435e+05    1.05706e+03    6.94051e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71326e+05    8.53033e+04   -3.86023e+05   -4.44933e+05    3.08755e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.80867e+01    1.39891e+02    1.95749e-05
> 
>            Step           Time
>           47000       94.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.71361e+03    7.72090e+02    5.08797e+02   -2.01174e+02    2.40151e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.06279e+04   -1.63308e+03   -5.67532e+05    1.01939e+03    7.04075e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70005e+05    8.48679e+04   -3.85137e+05   -4.44942e+05    3.07179e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82344e+01    7.48064e+00    1.99494e-05
> 
>            Step           Time
>           48000       96.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.68491e+03    7.76977e+02    5.50149e+02   -1.80872e+02    2.41223e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.10765e+04   -1.63352e+03   -5.69498e+05    1.02977e+03    6.89259e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71382e+05    8.58983e+04   -3.85484e+05   -4.44961e+05    3.10909e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.82766e+01   -7.11559e+01    2.09539e-05
> 
>            Step           Time
>           49000       98.00000
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.71026e+03    8.34841e+02    6.28228e+02   -2.24389e+02    2.40055e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.19025e+04   -1.63148e+03   -5.69486e+05    9.92246e+02    6.66952e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70601e+05    8.50578e+04   -3.85544e+05   -4.44965e+05    3.07866e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.80808e+01    8.29412e+01    2.05951e-05
> 
>            Step           Time
>           50000      100.00000
> 
> Writing checkpoint, step 50000 at Sun Aug 23 14:36:20 2020
> 
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.74603e+03    7.21018e+02    5.49238e+02   -2.04089e+02    2.39762e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.16884e+04   -1.63173e+03   -5.69559e+05    1.06642e+03    7.08281e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.70939e+05    8.57064e+04   -3.85233e+05   -4.44979e+05    3.10214e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81052e+01    9.31408e+01    2.12897e-05
> 
> 
> 	<======  ###############  ==>
> 	<====  A V E R A G E S  ====>
> 	<==  ###############  ======>
> 
> 	Statistics over 50001 steps using 501 frames
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     1.71569e+03    7.65816e+02    5.60979e+02   -1.91765e+02    2.40274e+04
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
>     7.13589e+04   -1.63238e+03   -5.69665e+05    1.04834e+03    7.04084e+02
>       Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
>    -4.71308e+05    8.56247e+04   -3.85684e+05   -4.44676e+05    3.09918e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -7.81677e+01   -3.90106e-01    0.00000e+00
> 
>           Box-X          Box-Y          Box-Z
>     6.58256e+00    4.37700e+00    1.20413e+01
> 
>    Total Virial (kJ/mol)
>     2.85988e+04   -2.43216e+02   -2.16895e+02
>    -2.43987e+02    2.85355e+04    1.87213e+02
>    -2.16744e+02    1.88318e+02    2.85011e+04
> 
>    Pressure (bar)
>    -3.91915e-01    2.51822e+01    2.29626e+01
>     2.52560e+01    7.24501e+00   -1.46705e+01
>     2.29479e+01   -1.47763e+01   -8.02342e+00
> 
>       T-Protein  T-non-Protein
>     3.09665e+02    3.09927e+02
> 
> 
> 	M E G A - F L O P S   A C C O U N T I N G
> 
>  NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
>  RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
>  W3=SPC/TIP3p  W4=TIP4p (single or pairs)
>  V&F=Potential and force  V=Potential only  F=Force only
> 
>  Computing:                               M-Number         M-Flops  % Flops
> -----------------------------------------------------------------------------
>  Pair Search distance check           12786.518692      115078.668     0.1
>  NxN Ewald Elec. + LJ [F]           1068744.793248    70537156.354    52.1
>  NxN Ewald Elec. + LJ [V&F]           10816.965216     1157415.278     0.9
>  NxN LJ [F]                            1345.367232       44397.119     0.0
>  NxN LJ [V&F]                            13.618496         585.595     0.0
>  NxN Ewald Elec. [F]                 987500.292768    60237517.859    44.5
>  NxN Ewald Elec. [V&F]                 9994.694176      839554.311     0.6
>  1,4 nonbonded interactions              94.501890        8505.170     0.0
>  Calc Weights                          4981.149621      179321.386     0.1
>  Spread Q Bspline                    106264.525248      212529.050     0.2
>  Gather F Bspline                    106264.525248      637587.151     0.5
>  3D-FFT                              155438.308704     1243506.470     0.9
>  Solve PME                               58.801176        3763.275     0.0
>  Shift-X                                 16.636707          99.820     0.0
>  Angles                                  82.751655       13902.278     0.0
>  Propers                                 28.750575        6583.882     0.0
>  Impropers                               28.000560        5824.116     0.0
>  Pos. Restr.                             46.000920        2300.046     0.0
>  Virial                                 332.553252        5985.959     0.0
>  Stop-CM                                 16.669914         166.699     0.0
>  P-Coupling                             332.103207        1992.619     0.0
>  Calc-Ekin                              664.206414       17933.573     0.0
>  Lincs                                   56.753405        3405.204     0.0
>  Lincs-Mat                              993.059580        3972.238     0.0
>  Constraint-V                          1714.818590       13718.549     0.0
>  Constraint-Vir                         331.633160        7959.196     0.0
>  Settle                                 533.782025      172411.594     0.1
> -----------------------------------------------------------------------------
>  Total                                               135473173.461   100.0
> -----------------------------------------------------------------------------
> 
> 
>      R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
> 
> On 1 MPI rank, each using 4 OpenMP threads
> 
>  Computing:          Num   Num      Call    Wall time         Giga-Cycles
>                      Ranks Threads  Count      (s)         total sum    %
> -----------------------------------------------------------------------------
>  Neighbor search        1    4        501      12.283        132.361   1.0
>  Force                  1    4      50001    1042.037      11228.525  87.9
>  PME mesh               1    4      50001      96.655       1041.511   8.2
>  NB X/F buffer ops.     1    4      99501      10.030        108.075   0.8
>  Write traj.            1    4         52       1.762         18.989   0.1
>  Update                 1    4      50001       5.096         54.917   0.4
>  Constraints            1    4      50003      13.055        140.672   1.1
>  Rest                                           3.986         42.950   0.3
> -----------------------------------------------------------------------------
>  Total                                       1184.904      12768.001 100.0
> -----------------------------------------------------------------------------
>  Breakdown of PME mesh computation
> -----------------------------------------------------------------------------
>  PME spread             1    4      50001      42.483        457.776   3.6
>  PME gather             1    4      50001      27.018        291.130   2.3
>  PME 3D-FFT             1    4     100002      24.533        264.358   2.1
>  PME solve Elec         1    4      50001       2.465         26.563   0.2
> -----------------------------------------------------------------------------
> 
>                Core t (s)   Wall t (s)        (%)
>        Time:     4739.612     1184.904      400.0
>                  (ns/day)    (hour/ns)
> Performance:        7.292        3.291
> Finished mdrun on rank 0 Sun Aug 23 14:36:20 2020

kw24 · August 30, 2020, 5:27pm

Faster run part 1

>                       :-) GROMACS - gmx mdrun, 2020.3 (-:
> 
>                             GROMACS is written by:
>      Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
>     Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
>  Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
>   Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
>   Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
>     Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
>   Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
>     Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
>     Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
>    Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
>  Christian Wennberg    Maarten Wolf      Artem Zhmurov   
>                            and the project leaders:
>         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> 
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2019, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
> 
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
> 
> GROMACS:      gmx mdrun, version 2020.3
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:  /Users/profile1
> Process ID:   18242
> Command line:
>   gmx mdrun -deffnm npt
> 
> GROMACS version:    2020.3
> Verified release checksum is c0599e547549c2d0ef4fc678dc5a26ad0000eab045e938fed756f9ff5b99a197
> Precision:          single
> Memory model:       64 bit
> MPI library:        thread_mpi
> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
> GPU support:        OpenCL
> SIMD instructions:  AVX2_256
> FFT library:        fftw-3.3.8-sse2
> RDTSCP usage:       enabled
> TNG support:        enabled
> Hwloc support:      disabled
> Tracing support:    disabled
> C compiler:         /usr/local/bin/icc Intel 19.1.2.20200623
> C compiler flags:   -march=core-avx2 -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG
> C++ compiler:       /usr/local/bin/icpc Intel 19.1.2.20200623
> C++ compiler flags: -march=core-avx2 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG
> OpenCL include dir: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/OpenCL.framework
> OpenCL library:     /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/OpenCL.framework
> OpenCL version:     1.2
> 
> 
> Running on 1 node with total 4 cores, 4 logical cores, 0 compatible GPUs
> Hardware detected:
>   CPU info:
>     Vendor: Intel
>     Brand:  Intel(R) Core(TM) i5-4570R CPU @ 2.70GHz
>     Family: 6   Model: 70   Stepping: 1
>     Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
>   Hardware topology: Only logical processor count
>   GPU info:
>     Number of GPUs detected: 1
>     #0: name: Iris Pro, vendor: Intel, device version: OpenCL 1.2 , stat: incompatible (please recompile with GMX_OPENCL_NB_CLUSTER_SIZE=4)
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
> Lindahl
> GROMACS: High performance molecular simulations through multi-level
> parallelism from laptops to supercomputers
> SoftwareX 1 (2015) pp. 19-25
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
> Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
> GROMACS
> In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
> Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
> GROMACS 4.5: a high-throughput and highly parallel open source molecular
> simulation toolkit
> Bioinformatics 29 (2013) pp. 845-54
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
> molecular simulation
> J. Chem. Theory Comput. 4 (2008) pp. 435-447
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
> Berendsen
> GROMACS: Fast, Flexible and Free
> J. Comp. Chem. 26 (2005) pp. 1701-1719
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> E. Lindahl and B. Hess and D. van der Spoel
> GROMACS 3.0: A package for molecular simulation and trajectory analysis
> J. Mol. Mod. 7 (2001) pp. 306-317
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> H. J. C. Berendsen, D. van der Spoel and R. van Drunen
> GROMACS: A message-passing parallel molecular dynamics implementation
> Comp. Phys. Comm. 91 (1995) pp. 43-56
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
> https://doi.org/10.5281/zenodo.3923645
> -------- -------- --- Thank You --- -------- --------
> 
> Input Parameters:
>    integrator                     = md
>    tinit                          = 0
>    dt                             = 0.002
>    nsteps                         = 50000
>    init-step                      = 0
>    simulation-part                = 1
>    comm-mode                      = Linear
>    nstcomm                        = 100
>    bd-fric                        = 0
>    ld-seed                        = 1160416371
>    emtol                          = 10
>    emstep                         = 0.01
>    niter                          = 20
>    fcstep                         = 0
>    nstcgsteep                     = 1000
>    nbfgscorr                      = 10
>    rtpi                           = 0.05
>    nstxout                        = 500
>    nstvout                        = 500
>    nstfout                        = 0
>    nstlog                         = 500
>    nstcalcenergy                  = 100
>    nstenergy                      = 500
>    nstxout-compressed             = 0
>    compressed-x-precision         = 1000
>    cutoff-scheme                  = Verlet
>    nstlist                        = 10
>    pbc                            = xyz
>    periodic-molecules             = false
>    verlet-buffer-tolerance        = 0.005
>    rlist                          = 1
>    coulombtype                    = PME
>    coulomb-modifier               = Potential-shift
>    rcoulomb-switch                = 0
>    rcoulomb                       = 1
>    epsilon-r                      = 1
>    epsilon-rf                     = inf
>    vdw-type                       = Cut-off
>    vdw-modifier                   = Potential-shift
>    rvdw-switch                    = 0
>    rvdw                           = 1
>    DispCorr                       = EnerPres
>    table-extension                = 1
>    fourierspacing                 = 0.16
>    fourier-nx                     = 44
>    fourier-ny                     = 44
>    fourier-nz                     = 44
>    pme-order                      = 4
>    ewald-rtol                     = 1e-05
>    ewald-rtol-lj                  = 0.001
>    lj-pme-comb-rule               = Geometric
>    ewald-geometry                 = 0
>    epsilon-surface                = 0
>    tcoupl                         = V-rescale
>    nsttcouple                     = 10
>    nh-chain-length                = 0
>    print-nose-hoover-chain-variables = false
>    pcoupl                         = Parrinello-Rahman
>    pcoupltype                     = Isotropic
>    nstpcouple                     = 10
>    tau-p                          = 2
>    compressibility (3x3):
>       compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
>       compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
>       compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
>    ref-p (3x3):
>       ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
>       ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
>       ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
>    refcoord-scaling               = COM
>    posres-com (3):
>       posres-com[0]= 4.97362e-01
>       posres-com[1]= 5.02071e-01
>       posres-com[2]= 4.99244e-01
>    posres-comB (3):
>       posres-comB[0]= 4.97362e-01
>       posres-comB[1]= 5.02071e-01
>       posres-comB[2]= 4.99244e-01
>    QMMM                           = false
>    QMconstraints                  = 0
>    QMMMscheme                     = 0
>    MMChargeScaleFactor            = 1
> qm-opts:
>    ngQM                           = 0
>    constraint-algorithm           = Lincs
>    continuation                   = true
>    Shake-SOR                      = false
>    shake-tol                      = 0.0001
>    lincs-order                    = 4
>    lincs-iter                     = 1
>    lincs-warnangle                = 30
>    nwall                          = 0
>    wall-type                      = 9-3
>    wall-r-linpot                  = -1
>    wall-atomtype[0]               = -1
>    wall-atomtype[1]               = -1
>    wall-density[0]                = 0
>    wall-density[1]                = 0
>    wall-ewald-zfac                = 3
>    pull                           = false
>    awh                            = false
>    rotation                       = false
>    interactiveMD                  = false
>    disre                          = No
>    disre-weighting                = Conservative
>    disre-mixed                    = false
>    dr-fc                          = 1000
>    dr-tau                         = 0
>    nstdisreout                    = 100
>    orire-fc                       = 0
>    orire-tau                      = 0
>    nstorireout                    = 100
>    free-energy                    = no
>    cos-acceleration               = 0
>    deform (3x3):
>       deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>       deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>       deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    simulated-tempering            = false
>    swapcoords                     = no
>    userint1                       = 0
>    userint2                       = 0
>    userint3                       = 0
>    userint4                       = 0
>    userreal1                      = 0
>    userreal2                      = 0
>    userreal3                      = 0
>    userreal4                      = 0
>    applied-forces:
>      electric-field:
>        x:
>          E0                       = 0
>          omega                    = 0
>          t0                       = 0
>          sigma                    = 0
>        y:
>          E0                       = 0
>          omega                    = 0
>          t0                       = 0
>          sigma                    = 0
>        z:
>          E0                       = 0
>          omega                    = 0
>          t0                       = 0
>          sigma                    = 0
>      density-guided-simulation:
>        active                     = false
>        group                      = protein
>        similarity-measure         = inner-product
>        atom-spreading-weight      = unity
>        force-constant             = 1e+09
>        gaussian-transform-spreading-width = 0.2
>        gaussian-transform-spreading-range-in-multiples-of-width = 4
>        reference-density-filename = reference.mrc
>        nst                        = 1
>        normalize-densities        = true
>        adaptive-force-scaling     = false
>        adaptive-force-scaling-time-constant = 4
> grpopts:
>    nrdf:     4920.79     63837.2
>    ref-t:         300         300
>    tau-t:         0.1         0.1
> annealing:          No          No
> annealing-npoints:           0           0
>    acc:	           0           0           0
>    nfreeze:           N           N           N
>    energygrp-flags[  0]: 0
> 
> Changing nstlist from 10 to 50, rlist from 1 to 1.115
> 
> Using 1 MPI thread
> Using 4 OpenMP threads 
> 
> System total charge: -0.000
> Will do PME sum in reciprocal space for electrostatic interactions.
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
> A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
> 
> Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
> Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
> Initialized non-bonded Ewald tables, spacing: 9.33e-04 size: 1073
> 
> Generated table with 1057 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1057 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1057 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
> 
> Using SIMD 4x8 nonbonded short-range kernels
> 
> Using a dual 4x8 pair-list setup updated with dynamic pruning:
>   outer list: updated every 50 steps, buffer 0.115 nm, rlist 1.115 nm
>   inner list: updated every 12 steps, buffer 0.002 nm, rlist 1.002 nm
> At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
>   outer list: updated every 50 steps, buffer 0.243 nm, rlist 1.243 nm
>   inner list: updated every 12 steps, buffer 0.047 nm, rlist 1.047 nm
> 
> Using geometric Lennard-Jones combination rule
> 
> Long Range LJ corr.: <C6> 3.1923e-04
> 
> 
> Initializing LINear Constraint Solver
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
> LINCS: A Linear Constraint Solver for molecular simulations
> J. Comp. Chem. 18 (1997) pp. 1463-1472
> -------- -------- --- Thank You --- -------- --------
> 
> The number of constraints is 959
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> S. Miyamoto and P. A. Kollman
> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
> Water Models
> J. Comp. Chem. 13 (1992) pp. 952-962
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> G. Bussi, D. Donadio and M. Parrinello
> Canonical sampling through velocity rescaling
> J. Chem. Phys. 126 (2007) pp. 014101
> -------- -------- --- Thank You --- -------- --------
> 
> There are: 33876 Atoms
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
>   0:  rest
> 
> Started mdrun on rank 0 Fri Aug 21 17:23:52 2020
> 
>            Step           Time
>               0        0.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.52464e+03    3.76919e+03    2.64593e+02    1.82436e+03    2.62883e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.65431e+03    9.04943e+04   -4.44920e+03   -6.29256e+05    2.94029e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     1.24347e-01   -5.22605e+05    8.61967e+04   -4.36408e+05   -4.36388e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01553e+02   -2.14729e+02   -6.69913e+02    2.71964e-06
> 
>            Step           Time
>             500        1.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.51940e+03    3.77569e+03    2.43113e+02    1.82836e+03    2.65996e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.66012e+03    9.25467e+04   -4.55333e+03   -6.32688e+05    2.96731e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.82369e+02   -5.23559e+05    8.60159e+04   -4.37543e+05   -4.36345e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00920e+02   -2.24884e+02   -1.12887e+02    2.80051e-06
> 
>            Step           Time
>            1000        2.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.44893e+03    3.75378e+03    2.40354e+02    1.83581e+03    2.66785e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.66829e+03    9.46087e+04   -4.56310e+03   -6.35523e+05    2.97816e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.02759e+02   -5.24381e+05    8.59991e+04   -4.38382e+05   -4.36362e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00861e+02   -2.25849e+02    3.25970e+02    2.76845e-06
> 
>            Step           Time
>            1500        3.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.55379e+03    3.75836e+03    2.50813e+02    1.88068e+03    2.70388e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.79177e+03    9.25365e+04   -4.56439e+03   -6.32584e+05    3.00557e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.20419e+02   -5.23247e+05    8.59962e+04   -4.37250e+05   -4.36364e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00851e+02   -2.25977e+02    1.05249e+01    2.49491e-06
> 
>            Step           Time
>            2000        4.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.43521e+03    3.87804e+03    2.38157e+02    1.86497e+03    2.76967e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.77768e+03    9.39256e+04   -4.53438e+03   -6.32969e+05    3.04783e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.57202e+02   -5.22109e+05    8.62405e+04   -4.35869e+05   -4.36359e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01706e+02   -2.23019e+02    1.61293e+02    2.88874e-06
> 
>            Step           Time
>            2500        5.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.59662e+03    3.76196e+03    2.73944e+02    1.79775e+03    2.63910e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.70413e+03    9.34997e+04   -4.56098e+03   -6.34006e+05    2.91134e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.98281e+02   -5.23884e+05    8.64655e+04   -4.37419e+05   -4.36370e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.02493e+02   -2.25640e+02   -1.89945e+02    2.66990e-06
> 
>            Step           Time
>            3000        6.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.49476e+03    3.71871e+03    2.36562e+02    1.83096e+03    2.57185e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.71933e+03    9.25080e+04   -4.58723e+03   -6.33637e+05    2.94208e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.67348e+02   -5.24734e+05    8.56363e+04   -4.39098e+05   -4.36366e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99592e+02   -2.28242e+02   -1.51194e+02    2.69972e-06
> 
>            Step           Time
>            3500        7.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.50228e+03    3.64318e+03    2.31144e+02    1.74992e+03    2.64446e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.65255e+03    9.27356e+04   -4.57472e+03   -6.33474e+05    2.92153e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.60429e+02   -5.24507e+05    8.53348e+04   -4.39172e+05   -4.36370e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.98537e+02   -2.27000e+02   -1.94729e+02    2.73251e-06
> 
>            Step           Time
>            4000        8.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.50207e+03    3.80960e+03    2.36965e+02    1.87508e+03    2.67649e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69072e+03    9.45735e+04   -4.57168e+03   -6.36623e+05    2.90928e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.19341e+02   -5.25402e+05    8.54593e+04   -4.39943e+05   -4.36364e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.98973e+02   -2.26699e+02    1.21145e+02    2.79602e-06
> 
>            Step           Time
>            4500        9.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46655e+03    3.72458e+03    2.68898e+02    1.75447e+03    2.65616e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.59202e+03    9.38683e+04   -4.54587e+03   -6.34681e+05    3.02869e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.17861e+02   -5.24349e+05    8.65466e+04   -4.37802e+05   -4.36394e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.02777e+02   -2.24149e+02    9.29454e+00    2.59174e-06
> 
>            Step           Time
>            5000       10.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.49648e+03    3.69394e+03    2.17336e+02    1.82790e+03    2.69462e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69887e+03    9.37222e+04   -4.56635e+03   -6.35423e+05    2.97937e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.96754e+02   -5.25162e+05    8.53938e+04   -4.39768e+05   -4.36377e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.98744e+02   -2.26171e+02   -4.35343e+01    2.75426e-06
> 
>            Step           Time
>            5500       11.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.45378e+03    3.75460e+03    2.18654e+02    1.78888e+03    2.65144e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.75544e+03    9.24059e+04   -4.55570e+03   -6.32780e+05    3.02819e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.94955e+02   -5.23784e+05    8.70565e+04   -4.36727e+05   -4.36408e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.04561e+02   -2.25118e+02   -2.06250e+02    3.06994e-06
> 
>            Step           Time
>            6000       12.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.47942e+03    3.76163e+03    2.48667e+02    1.82641e+03    2.64213e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.75039e+03    9.29812e+04   -4.54941e+03   -6.35084e+05    2.89716e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.58008e+02   -5.25588e+05    8.65999e+04   -4.38988e+05   -4.36389e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.02963e+02   -2.24498e+02   -1.68161e+02    2.81055e-06
> 
>            Step           Time
>            6500       13.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.43328e+03    3.63710e+03    2.58858e+02    1.79000e+03    2.63708e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.79417e+03    9.41165e+04   -4.54953e+03   -6.34483e+05    2.90449e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.03755e+02   -5.23958e+05    8.56865e+04   -4.38271e+05   -4.36396e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99768e+02   -2.24509e+02    1.42418e+01    3.05583e-06
> 
>            Step           Time
>            7000       14.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.49187e+03    3.74095e+03    2.58905e+02    1.80769e+03    2.64420e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.80860e+03    9.41604e+04   -4.56533e+03   -6.36401e+05    2.91605e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.55924e+02   -5.25682e+05    8.59714e+04   -4.39710e+05   -4.36399e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00765e+02   -2.26070e+02   -1.18018e+02    2.85990e-06
> 
>            Step           Time
>            7500       15.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.44623e+03    3.94895e+03    2.74462e+02    1.84960e+03    2.68035e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.71117e+03    9.36895e+04   -4.54981e+03   -6.33830e+05    2.91085e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.70823e+02   -5.23398e+05    8.57606e+04   -4.37638e+05   -4.36403e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00027e+02   -2.24537e+02   -3.10528e+01    2.99103e-06
> 
>            Step           Time
>            8000       16.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.41538e+03    3.91546e+03    2.26046e+02    1.89653e+03    2.62569e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.74726e+03    9.34538e+04   -4.55611e+03   -6.34152e+05    2.87703e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.91374e+02   -5.24059e+05    8.48425e+04   -4.39217e+05   -4.36380e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.96815e+02   -2.25159e+02   -9.99352e+01    2.65134e-06
> 
>            Step           Time
>            8500       17.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.53482e+03    3.69646e+03    2.33544e+02    1.83958e+03    2.64866e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.77670e+03    9.37912e+04   -4.54322e+03   -6.35780e+05    2.96110e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.54744e+02   -5.25387e+05    8.52558e+04   -4.40131e+05   -4.36388e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.98261e+02   -2.23888e+02   -9.26919e+01    2.93991e-06
> 
>            Step           Time
>            9000       18.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.44565e+03    3.83833e+03    2.66098e+02    1.78034e+03    2.66713e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.68807e+03    9.37544e+04   -4.57688e+03   -6.34438e+05    2.86600e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.09797e+02   -5.24199e+05    8.56893e+04   -4.38509e+05   -4.36379e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99778e+02   -2.27214e+02   -2.93022e+01    2.88007e-06
>

kw24 · August 30, 2020, 5:28pm

Faster run part 2

>            Step           Time
>            9500       19.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.35849e+03    3.72532e+03    2.55775e+02    1.88263e+03    2.65547e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.70958e+03    9.33944e+04   -4.53557e+03   -6.34516e+05    2.91260e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.04056e+02   -5.24654e+05    8.52987e+04   -4.39355e+05   -4.36392e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.98411e+02   -2.23136e+02   -1.16328e+02    3.44645e-06
> 
>            Step           Time
>           10000       20.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.52478e+03    3.69122e+03    2.66490e+02    1.87160e+03    2.69519e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.78389e+03    9.35412e+04   -4.55349e+03   -6.33237e+05    2.93832e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.02572e+02   -5.22975e+05    8.55612e+04   -4.37414e+05   -4.36395e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99330e+02   -2.24901e+02    9.59448e+01    3.38927e-06
> 
>            Step           Time
>           10500       21.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.43883e+03    3.77784e+03    2.46974e+02    1.77086e+03    2.68555e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.63816e+03    9.37081e+04   -4.58400e+03   -6.34795e+05    2.97892e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.40253e+02   -5.24693e+05    8.56131e+04   -4.39080e+05   -4.36383e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99511e+02   -2.27921e+02    1.53291e+02    2.88386e-06
> 
>            Step           Time
>           11000       22.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.42190e+03    3.70599e+03    2.33190e+02    1.77383e+03    2.74118e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69012e+03    9.17090e+04   -4.55292e+03   -6.31699e+05    2.93358e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.71777e+02   -5.23572e+05    8.57524e+04   -4.37819e+05   -4.36398e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99999e+02   -2.24844e+02   -2.82846e+02    2.94663e-06
> 
>            Step           Time
>           11500       23.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.52972e+03    3.62973e+03    2.63997e+02    1.84628e+03    2.63130e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.76180e+03    9.48066e+04   -4.57260e+03   -6.35295e+05    2.88134e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.97014e+02   -5.24020e+05    8.57493e+04   -4.38270e+05   -4.36384e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99988e+02   -2.26790e+02    2.21116e+02    3.54973e-06
> 
>            Step           Time
>           12000       24.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46025e+03    3.74615e+03    2.33337e+02    1.79373e+03    2.65633e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.70124e+03    9.38365e+04   -4.57327e+03   -6.35304e+05    2.84605e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.93941e+02   -5.25110e+05    8.53980e+04   -4.39712e+05   -4.36386e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.98759e+02   -2.26856e+02    3.70665e+01    2.72705e-06
> 
>            Step           Time
>           12500       25.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.51990e+03    3.83281e+03    2.72730e+02    1.78173e+03    2.70273e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.76622e+03    9.34164e+04   -4.56210e+03   -6.35432e+05    3.01584e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.71625e+02   -5.25215e+05    8.63440e+04   -4.38871e+05   -4.36409e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.02068e+02   -2.25751e+02    3.03448e+01    2.98991e-06
> 
>            Step           Time
>           13000       26.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.49673e+03    3.67939e+03    2.47467e+02    1.93557e+03    2.67493e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.74656e+03    9.36235e+04   -4.55047e+03   -6.34553e+05    2.97527e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.64846e+02   -5.24260e+05    8.58359e+04   -4.38424e+05   -4.36396e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00291e+02   -2.24603e+02    3.22473e+00    2.62978e-06
> 
>            Step           Time
>           13500       27.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.53077e+03    3.69240e+03    2.35421e+02    1.82465e+03    2.66371e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.67281e+03    9.32996e+04   -4.55879e+03   -6.34593e+05    2.91286e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.49031e+02   -5.24870e+05    8.61928e+04   -4.38677e+05   -4.36407e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01539e+02   -2.25424e+02   -5.80253e+01    3.07316e-06
> 
>            Step           Time
>           14000       28.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.50002e+03    3.75564e+03    2.21980e+02    1.82001e+03    2.61690e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.75147e+03    9.37865e+04   -4.55346e+03   -6.35147e+05    2.92781e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.60670e+02   -5.24859e+05    8.58155e+04   -4.39044e+05   -4.36406e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00219e+02   -2.24897e+02   -5.09190e+01    3.00452e-06
> 
>            Step           Time
>           14500       29.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.43565e+03    3.68395e+03    2.62261e+02    1.78240e+03    2.68611e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.77787e+03    9.41967e+04   -4.56541e+03   -6.35808e+05    2.93684e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.27413e+02   -5.25184e+05    8.65745e+04   -4.38609e+05   -4.36419e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.02875e+02   -2.26078e+02    1.22749e+02    2.64901e-06
> 
>            Step           Time
>           15000       30.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.39565e+03    3.73507e+03    2.42486e+02    1.73720e+03    2.71579e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.81018e+03    9.36374e+04   -4.56541e+03   -6.35416e+05    2.89715e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.67501e+02   -5.25343e+05    8.52530e+04   -4.40090e+05   -4.36422e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.98251e+02   -2.26078e+02    8.05608e+01    2.81208e-06
> 
>            Step           Time
>           15500       31.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.45757e+03    3.75759e+03    2.21503e+02    1.77610e+03    2.71982e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.70290e+03    9.25636e+04   -4.54824e+03   -6.32468e+05    2.96651e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.04264e+02   -5.23347e+05    8.56247e+04   -4.37722e+05   -4.36445e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99552e+02   -2.24382e+02   -1.25337e+02    3.03200e-06
> 
>            Step           Time
>           16000       32.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.50782e+03    3.85076e+03    2.41777e+02    1.72908e+03    2.68250e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.73983e+03    9.29982e+04   -4.56883e+03   -6.33123e+05    2.97180e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.63825e+02   -5.23506e+05    8.56827e+04   -4.37823e+05   -4.36407e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99754e+02   -2.26416e+02    7.88932e+01    2.69295e-06
> 
>            Step           Time
>           16500       33.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.45951e+03    3.84964e+03    2.55045e+02    1.84206e+03    2.64001e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69513e+03    9.28938e+04   -4.56254e+03   -6.33586e+05    3.05261e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.76450e+02   -5.23984e+05    8.59406e+04   -4.38043e+05   -4.36426e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00657e+02   -2.25794e+02   -9.44006e+01    3.37194e-06
> 
>            Step           Time
>           17000       34.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.43602e+03    3.73273e+03    2.29234e+02    1.84260e+03    2.64913e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.71555e+03    9.44964e+04   -4.57351e+03   -6.36885e+05    2.97789e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.52055e+02   -5.25927e+05    8.57402e+04   -4.40187e+05   -4.36425e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99956e+02   -2.26880e+02    1.40022e+02    3.00804e-06
> 
>            Step           Time
>           17500       35.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.49714e+03    3.74945e+03    2.38448e+02    1.79539e+03    2.58624e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69006e+03    9.38088e+04   -4.56503e+03   -6.35419e+05    2.95637e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.69961e+02   -5.25192e+05    8.60367e+04   -4.39155e+05   -4.36434e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00993e+02   -2.26040e+02   -1.20077e+02    2.87859e-06
> 
>            Step           Time
>           18000       36.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.38369e+03    3.73653e+03    2.70676e+02    1.84109e+03    2.71333e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.77034e+03    9.32684e+04   -4.54489e+03   -6.34350e+05    2.88242e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.30845e+02   -5.24597e+05    8.55043e+04   -4.39093e+05   -4.36414e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99130e+02   -2.24053e+02    8.03746e+01    2.73118e-06
> 
>            Step           Time
>           18500       37.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.37138e+03    3.65758e+03    2.56642e+02    1.82013e+03    2.76698e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.76043e+03    9.28682e+04   -4.55490e+03   -6.33987e+05    2.88746e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.42511e+02   -5.24711e+05    8.63153e+04   -4.38396e+05   -4.36436e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01968e+02   -2.25040e+02   -3.27070e+01    3.11844e-06
> 
>            Step           Time
>           19000       38.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.30290e+03    3.83048e+03    2.58412e+02    1.79506e+03    2.72509e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.85621e+03    9.36138e+04   -4.58075e+03   -6.35226e+05    2.99345e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.54556e+02   -5.24977e+05    8.67049e+04   -4.38272e+05   -4.36444e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.03331e+02   -2.27598e+02    2.52427e+02    3.14199e-06
> 
>            Step           Time
>           19500       39.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46791e+03    3.81160e+03    2.14292e+02    1.79952e+03    2.61097e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.64627e+03    9.37364e+04   -4.56124e+03   -6.35251e+05    2.86210e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.45338e+02   -5.25218e+05    8.55344e+04   -4.39684e+05   -4.36434e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99236e+02   -2.25666e+02    2.54648e+00    2.72076e-06
> 
>            Step           Time
>           20000       40.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46026e+03    3.73567e+03    2.69806e+02    1.79002e+03    2.69556e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.68632e+03    9.36193e+04   -4.56732e+03   -6.35175e+05    2.91685e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.47569e+02   -5.25121e+05    8.49844e+04   -4.40137e+05   -4.36418e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.97311e+02   -2.26267e+02    3.33348e+01    2.67771e-06
> 
>            Step           Time
>           20500       41.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.44582e+03    3.66860e+03    2.54216e+02    1.91826e+03    2.65868e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.76659e+03    9.40614e+04   -4.56160e+03   -6.35722e+05    2.90821e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.49314e+02   -5.25053e+05    8.54831e+04   -4.39570e+05   -4.36436e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99056e+02   -2.25701e+02   -7.51953e-02    3.11748e-06
> 
>            Step           Time
>           21000       42.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.45421e+03    3.59178e+03    2.72922e+02    1.86326e+03    2.64376e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.62335e+03    9.35296e+04   -4.57520e+03   -6.34282e+05    2.93218e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.05199e+02   -5.24441e+05    8.46464e+04   -4.39794e+05   -4.36414e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.96129e+02   -2.27047e+02    8.15097e+00    3.08325e-06
> 
>            Step           Time
>           21500       43.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.41179e+03    3.72147e+03    2.55266e+02    1.86001e+03    2.66530e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.75471e+03    9.32357e+04   -4.56246e+03   -6.33709e+05    2.89833e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.09524e+02   -5.23959e+05    8.55270e+04   -4.38432e+05   -4.36435e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99210e+02   -2.25786e+02   -8.29007e+01    2.83936e-06
> 
>            Step           Time
>           22000       44.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.43835e+03    3.71462e+03    2.47685e+02    1.82545e+03    2.70860e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.79714e+03    9.32717e+04   -4.57517e+03   -6.35301e+05    2.97834e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.53264e+02   -5.25441e+05    8.57937e+04   -4.39647e+05   -4.36443e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00143e+02   -2.27044e+02   -5.40075e+01    2.81035e-06
> 
>            Step           Time
>           22500       45.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.49477e+03    3.68742e+03    2.36980e+02    1.80871e+03    2.61922e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.74015e+03    9.42805e+04   -4.56036e+03   -6.35620e+05    2.93919e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.61521e+02   -5.24912e+05    8.56577e+04   -4.39254e+05   -4.36443e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99667e+02   -2.25579e+02    5.87313e+01    3.07438e-06
> 
>            Step           Time
>           23000       46.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.40983e+03    3.58604e+03    2.34931e+02    1.84613e+03    2.70340e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.78117e+03    9.34752e+04   -4.54355e+03   -6.34335e+05    2.90435e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.73680e+02   -5.24464e+05    8.59891e+04   -4.38474e+05   -4.36440e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00826e+02   -2.23921e+02   -5.01217e+01    3.11243e-06
> 
>            Step           Time
>           23500       47.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.40948e+03    3.91399e+03    2.49152e+02    1.83533e+03    2.61592e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.74019e+03    9.39987e+04   -4.56295e+03   -6.35136e+05    2.92640e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.50199e+02   -5.24560e+05    8.63379e+04   -4.38222e+05   -4.36437e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.02047e+02   -2.25835e+02   -1.43151e+01    2.51106e-06
> 
>            Step           Time
>           24000       48.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.44865e+03    3.79686e+03    2.92670e+02    1.82491e+03    2.69304e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.75965e+03    9.41739e+04   -4.57576e+03   -6.36269e+05    2.97706e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.79605e+02   -5.25398e+05    8.62602e+04   -4.39138e+05   -4.36449e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01775e+02   -2.27103e+02    2.70140e+02    3.01343e-06
> 
>            Step           Time
>           24500       49.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.40395e+03    3.61713e+03    2.20602e+02    1.83452e+03    2.66637e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.79356e+03    9.31645e+04   -4.56513e+03   -6.34527e+05    3.00848e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.44554e+02   -5.24939e+05    8.50127e+04   -4.39926e+05   -4.36442e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.97411e+02   -2.26050e+02   -6.48833e+01    2.99762e-06
> 
>            Step           Time
>           25000       50.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.48647e+03    3.56473e+03    2.33232e+02    1.78286e+03    2.65691e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.76970e+03    9.19994e+04   -4.57135e+03   -6.33424e+05    2.92082e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     3.99770e+02   -5.25181e+05    8.51411e+04   -4.40040e+05   -4.36439e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.97860e+02   -2.26665e+02   -2.01226e+02    2.85393e-06
> 
>            Step           Time
>           25500       51.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.44749e+03    3.67318e+03    2.72336e+02    1.74249e+03    2.68532e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.79452e+03    9.24031e+04   -4.56922e+03   -6.32411e+05    2.85299e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.84113e+02   -5.23625e+05    8.58545e+04   -4.37770e+05   -4.36442e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00356e+02   -2.26455e+02   -5.67573e+01    3.05650e-06
> 
>            Step           Time
>           26000       52.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.57064e+03    3.80937e+03    2.67644e+02    1.79884e+03    2.61556e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.65071e+03    9.32814e+04   -4.56000e+03   -6.33520e+05    2.99039e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.58936e+02   -5.23636e+05    8.64714e+04   -4.37165e+05   -4.36428e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.02514e+02   -2.25543e+02   -3.92290e+01    2.85402e-06
> 
>            Step           Time
>           26500       53.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.42722e+03    3.83878e+03    2.43717e+02    1.78822e+03    2.68952e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.75953e+03    9.36361e+04   -4.58169e+03   -6.34847e+05    2.96702e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.33462e+02   -5.24545e+05    8.63239e+04   -4.38221e+05   -4.36435e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01998e+02   -2.27692e+02    1.56129e+02    2.64557e-06
> 
>            Step           Time
>           27000       54.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.58585e+03    3.59373e+03    2.56901e+02    1.75951e+03    2.71252e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.72179e+03    9.34635e+04   -4.55078e+03   -6.34851e+05    2.91403e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.84560e+02   -5.24910e+05    8.57329e+04   -4.39177e+05   -4.36427e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99930e+02   -2.24633e+02   -1.16244e+02    2.79355e-06
> 
>            Step           Time
>           27500       55.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.38930e+03    3.67588e+03    2.56804e+02    1.84326e+03    2.65145e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.68335e+03    9.36003e+04   -4.56737e+03   -6.35007e+05    2.90101e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.70125e+02   -5.25103e+05    8.60234e+04   -4.39080e+05   -4.36451e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00947e+02   -2.26272e+02    3.18494e+01    3.03534e-06
> 
>            Step           Time
>           28000       56.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46313e+03    3.74736e+03    2.53708e+02    1.83427e+03    2.70741e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.74559e+03    9.44309e+04   -4.54498e+03   -6.36010e+05    2.98443e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.52582e+02   -5.24936e+05    8.61089e+04   -4.38827e+05   -4.36452e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01246e+02   -2.24062e+02    8.22661e+01    2.74010e-06
>

kw24 · August 30, 2020, 5:29pm

Faster run part 3

>            Step           Time
>           28500       57.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.40590e+03    3.80198e+03    2.35856e+02    1.73854e+03    2.60332e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.68529e+03    9.46906e+04   -4.57308e+03   -6.36285e+05    2.96487e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.16517e+02   -5.25216e+05    8.47125e+04   -4.40503e+05   -4.36439e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.96360e+02   -2.26837e+02    3.85315e+01    3.02074e-06
> 
>            Step           Time
>           29000       58.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.32863e+03    3.76344e+03    2.58700e+02    1.79728e+03    2.72301e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.66112e+03    9.36277e+04   -4.56581e+03   -6.35447e+05    2.87419e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.33982e+02   -5.25545e+05    8.58179e+04   -4.39727e+05   -4.36462e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00227e+02   -2.26117e+02    1.89423e+02    2.98735e-06
> 
>            Step           Time
>           29500       59.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.26607e+03    3.76193e+03    2.52217e+02    1.93290e+03    2.62181e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.72272e+03    9.38504e+04   -4.56080e+03   -6.34719e+05    2.87706e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.70395e+02   -5.24524e+05    8.51307e+04   -4.39393e+05   -4.36449e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.97823e+02   -2.25622e+02    7.96973e+01    3.12026e-06
> 
>            Step           Time
>           30000       60.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.32200e+03    3.78257e+03    2.79395e+02    1.85208e+03    2.64991e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.74608e+03    9.46642e+04   -4.56006e+03   -6.35367e+05    2.97438e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.08244e+02   -5.24148e+05    8.68158e+04   -4.37332e+05   -4.36483e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.03719e+02   -2.25548e+02    2.75595e+02    3.24424e-06
> 
>            Step           Time
>           30500       61.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.54361e+03    3.77021e+03    2.60749e+02    1.84382e+03    2.60127e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.70992e+03    9.41785e+04   -4.54052e+03   -6.35290e+05    2.92068e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.10091e+02   -5.24492e+05    8.57624e+04   -4.38730e+05   -4.36450e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00033e+02   -2.23623e+02   -1.65834e+02    2.59698e-06
> 
>            Step           Time
>           31000       62.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.60844e+03    3.80653e+03    2.36737e+02    1.76080e+03    2.61768e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.77691e+03    9.21563e+04   -4.54899e+03   -6.31847e+05    2.99500e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.54819e+02   -5.22983e+05    8.62731e+04   -4.36710e+05   -4.36462e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01820e+02   -2.24456e+02   -3.57154e+02    3.75545e-06
> 
>            Step           Time
>           31500       63.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.32901e+03    3.73620e+03    2.55845e+02    1.89904e+03    2.59370e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69008e+03    9.38059e+04   -4.55622e+03   -6.34259e+05    2.91896e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.79561e+02   -5.24107e+05    8.55234e+04   -4.38584e+05   -4.36462e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99197e+02   -2.25170e+02    1.61621e+01    2.80740e-06
> 
>            Step           Time
>           32000       64.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.37012e+03    3.79777e+03    2.69458e+02    1.79935e+03    2.65124e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.64349e+03    9.31854e+04   -4.57057e+03   -6.33664e+05    3.00543e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.58404e+02   -5.24053e+05    8.50107e+04   -4.39043e+05   -4.36448e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.97403e+02   -2.26589e+02    7.17918e+01    2.49190e-06
> 
>            Step           Time
>           32500       65.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46988e+03    3.81735e+03    2.47971e+02    1.77544e+03    2.55226e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.66512e+03    9.30230e+04   -4.54911e+03   -6.32555e+05    2.89075e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.50772e+02   -5.23212e+05    8.51471e+04   -4.38064e+05   -4.36461e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.97881e+02   -2.24468e+02   -2.10929e+02    3.07383e-06
> 
>            Step           Time
>           33000       66.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.43726e+03    3.84709e+03    2.46777e+02    1.88151e+03    2.71315e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.75770e+03    9.41790e+04   -4.57397e+03   -6.34915e+05    2.94342e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.83005e+02   -5.24000e+05    8.55989e+04   -4.38402e+05   -4.36438e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99461e+02   -2.26926e+02    1.72285e+02    2.96294e-06
> 
>            Step           Time
>           33500       67.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46390e+03    3.83240e+03    2.58621e+02    1.73032e+03    2.69794e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.80726e+03    9.33606e+04   -4.57713e+03   -6.34944e+05    2.93768e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.48522e+02   -5.24984e+05    8.58542e+04   -4.39130e+05   -4.36461e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00354e+02   -2.27239e+02    9.85938e+01    3.14077e-06
> 
>            Step           Time
>           34000       68.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.41545e+03    3.71788e+03    2.37981e+02    1.77999e+03    2.71440e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.70364e+03    9.38312e+04   -4.55419e+03   -6.35371e+05    2.92900e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.94119e+02   -5.25101e+05    8.59306e+04   -4.39171e+05   -4.36454e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00622e+02   -2.24969e+02    1.17900e+02    2.62090e-06
> 
>            Step           Time
>           34500       69.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46352e+03    3.80797e+03    2.55091e+02    1.85073e+03    2.72146e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.72530e+03    9.58257e+04   -4.55940e+03   -6.36481e+05    2.94878e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.76766e+02   -5.23965e+05    8.66612e+04   -4.37304e+05   -4.36462e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.03178e+02   -2.25484e+02    4.39094e+02    3.24747e-06
> 
>            Step           Time
>           35000       70.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.42650e+03    3.66713e+03    2.69469e+02    1.86022e+03    2.64904e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69603e+03    9.37728e+04   -4.54694e+03   -6.33620e+05    2.94657e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.49211e+02   -5.23430e+05    8.55671e+04   -4.37863e+05   -4.36452e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99350e+02   -2.24254e+02    3.58272e+01    2.96500e-06
> 
>            Step           Time
>           35500       71.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.42596e+03    3.89113e+03    2.13317e+02    1.94187e+03    2.66793e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69700e+03    9.39372e+04   -4.55680e+03   -6.33532e+05    2.87356e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.64347e+02   -5.22976e+05    8.58100e+04   -4.37166e+05   -4.36448e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00200e+02   -2.25227e+02    1.07192e+02    3.26102e-06
> 
>            Step           Time
>           36000       72.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.38712e+03    3.70536e+03    2.16812e+02    1.80945e+03    2.62666e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69786e+03    9.38900e+04   -4.55497e+03   -6.35450e+05    2.89149e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.68605e+02   -5.25312e+05    8.50317e+04   -4.40280e+05   -4.36448e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.97477e+02   -2.25046e+02   -2.40068e+01    2.85987e-06
> 
>            Step           Time
>           36500       73.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.42036e+03    3.77205e+03    2.41187e+02    1.80927e+03    2.67566e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.62610e+03    9.36861e+04   -4.55726e+03   -6.34382e+05    2.91603e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.06753e+02   -5.24386e+05    8.61054e+04   -4.38280e+05   -4.36465e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01233e+02   -2.25272e+02    8.05118e+00    2.84658e-06
> 
>            Step           Time
>           37000       74.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.51203e+03    3.73057e+03    2.52668e+02    1.80030e+03    2.67241e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.74815e+03    9.34677e+04   -4.55557e+03   -6.33703e+05    2.92897e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.19254e+02   -5.23627e+05    8.49805e+04   -4.38646e+05   -4.36469e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.97298e+02   -2.25105e+02   -4.13512e+01    2.98458e-06
> 
>            Step           Time
>           37500       75.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.50720e+03    3.75248e+03    2.70429e+02    1.83620e+03    2.66814e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.70495e+03    9.29836e+04   -4.56391e+03   -6.33863e+05    2.87997e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.45970e+02   -5.24378e+05    8.67333e+04   -4.37645e+05   -4.36482e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.03430e+02   -2.25929e+02   -6.56193e+01    2.86115e-06
> 
>            Step           Time
>           38000       76.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.45689e+03    3.68001e+03    2.47161e+02    1.80896e+03    2.69736e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.81995e+03    9.30119e+04   -4.55143e+03   -6.34316e+05    2.89909e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.70195e+02   -5.24775e+05    8.61348e+04   -4.38641e+05   -4.36474e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01336e+02   -2.24697e+02   -8.74013e+01    2.98819e-06
> 
>            Step           Time
>           38500       77.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.45031e+03    3.64766e+03    1.94278e+02    1.86336e+03    2.63102e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.70460e+03    9.36037e+04   -4.57088e+03   -6.34488e+05    2.91139e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.42169e+02   -5.24610e+05    8.61350e+04   -4.38475e+05   -4.36492e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01337e+02   -2.26619e+02    6.44847e+01    3.01611e-06
> 
>            Step           Time
>           39000       78.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.47519e+03    3.67085e+03    2.68145e+02    1.85210e+03    2.75435e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.81589e+03    9.31105e+04   -4.54797e+03   -6.33851e+05    3.02354e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.80537e+02   -5.23948e+05    8.55288e+04   -4.38419e+05   -4.36476e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99216e+02   -2.24356e+02   -1.78618e+02    2.74287e-06
> 
>            Step           Time
>           39500       79.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.52976e+03    3.93552e+03    2.19094e+02    1.79855e+03    2.59345e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.70177e+03    9.15895e+04   -4.55740e+03   -6.31267e+05    2.93948e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.68082e+02   -5.23049e+05    8.55775e+04   -4.37472e+05   -4.36470e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99387e+02   -2.25287e+02   -1.53998e+02    2.87130e-06
> 
>            Step           Time
>           40000       80.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.52917e+03    3.70792e+03    2.47134e+02    1.84674e+03    2.70111e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.71927e+03    9.37306e+04   -4.55799e+03   -6.34933e+05    2.81047e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.37346e+02   -5.24761e+05    8.49715e+04   -4.39790e+05   -4.36457e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.97267e+02   -2.25345e+02    4.19948e+00    2.60915e-06
> 
>            Step           Time
>           40500       81.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.51632e+03    3.75773e+03    2.50186e+02    1.84354e+03    2.62849e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.64296e+03    9.41841e+04   -4.56527e+03   -6.35549e+05    2.91529e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.78440e+02   -5.24897e+05    8.65806e+04   -4.38316e+05   -4.36485e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.02896e+02   -2.26064e+02   -9.73210e+01    3.26469e-06
> 
>            Step           Time
>           41000       82.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.42901e+03    3.88839e+03    2.61164e+02    1.84990e+03    2.70405e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.81613e+03    9.30781e+04   -4.55387e+03   -6.33880e+05    2.98900e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.79239e+02   -5.23938e+05    8.54084e+04   -4.38530e+05   -4.36457e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.98795e+02   -2.24938e+02    2.80143e+01    3.05857e-06
> 
>            Step           Time
>           41500       83.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.42597e+03    3.66167e+03    2.29538e+02    1.78817e+03    2.73337e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.77643e+03    9.47727e+04   -4.58132e+03   -6.35889e+05    2.97522e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.59535e+02   -5.24648e+05    8.66015e+04   -4.38046e+05   -4.36485e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.02969e+02   -2.27655e+02    3.34146e+02    2.88279e-06
> 
>            Step           Time
>           42000       84.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.45785e+03    3.77649e+03    2.28511e+02    1.79379e+03    2.65852e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.72150e+03    9.20792e+04   -4.55174e+03   -6.31175e+05    2.99065e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.15267e+02   -5.22505e+05    8.59833e+04   -4.36521e+05   -4.36490e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00806e+02   -2.24728e+02   -2.44269e+02    2.88970e-06
> 
>            Step           Time
>           42500       85.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.50102e+03    3.56996e+03    2.73461e+02    1.90791e+03    2.64384e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.75474e+03    9.37184e+04   -4.56172e+03   -6.34266e+05    2.97666e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.51503e+02   -5.24030e+05    8.55973e+04   -4.38433e+05   -4.36483e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99456e+02   -2.25713e+02   -2.05187e+01    3.16578e-06

kw24 · August 30, 2020, 5:29pm

Faster run part 4

>            Step           Time
>           43000       86.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46004e+03    3.73531e+03    2.19535e+02    1.85672e+03    2.60713e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.72905e+03    9.22348e+04   -4.55455e+03   -6.33392e+05    2.93599e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.39450e+02   -5.24729e+05    8.55969e+04   -4.39132e+05   -4.36482e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99454e+02   -2.25005e+02   -1.99435e+02    2.79909e-06
> 
>            Step           Time
>           43500       87.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46228e+03    3.85688e+03    2.70460e+02    1.79616e+03    2.65788e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.76089e+03    9.15369e+04   -4.54848e+03   -6.30884e+05    2.97536e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.35659e+02   -5.22680e+05    8.59162e+04   -4.36764e+05   -4.36495e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00571e+02   -2.24406e+02   -3.81121e+02    3.08304e-06
> 
>            Step           Time
>           44000       88.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.54523e+03    3.58108e+03    2.37378e+02    1.84904e+03    2.61611e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.73858e+03    9.23422e+04   -4.57953e+03   -6.32888e+05    2.98648e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.53815e+02   -5.24118e+05    8.57861e+04   -4.38332e+05   -4.36469e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00116e+02   -2.27477e+02   -9.14342e+01    2.86713e-06
> 
>            Step           Time
>           44500       89.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.40488e+03    3.77779e+03    2.72116e+02    1.85119e+03    2.65113e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.71842e+03    9.26746e+04   -4.56840e+03   -6.33264e+05    2.95900e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.00997e+02   -5.24023e+05    8.55558e+04   -4.38467e+05   -4.36474e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99311e+02   -2.26374e+02   -5.94689e+01    2.93647e-06
> 
>            Step           Time
>           45000       90.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.48374e+03    3.66997e+03    2.25076e+02    1.86593e+03    2.60690e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69155e+03    9.47721e+04   -4.54702e+03   -6.35961e+05    2.93542e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.42990e+02   -5.24814e+05    8.56164e+04   -4.39198e+05   -4.36477e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99523e+02   -2.24263e+02   -2.54143e+01    2.93672e-06
> 
>            Step           Time
>           45500       91.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.44961e+03    3.67503e+03    2.55489e+02    1.87331e+03    2.67719e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.78277e+03    9.38096e+04   -4.58318e+03   -6.34712e+05    2.88483e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.40110e+02   -5.24447e+05    8.57228e+04   -4.38724e+05   -4.36480e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99895e+02   -2.27839e+02    1.61072e+02    2.93484e-06
> 
>            Step           Time
>           46000       92.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.50844e+03    3.65262e+03    2.66285e+02    1.83635e+03    2.65325e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.73813e+03    9.23720e+04   -4.56344e+03   -6.32649e+05    2.90405e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.46582e+02   -5.23835e+05    8.51223e+04   -4.38712e+05   -4.36473e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.97794e+02   -2.25883e+02   -1.88967e+02    3.26391e-06
> 
>            Step           Time
>           46500       93.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.47743e+03    3.75969e+03    2.51564e+02    1.85838e+03    2.62982e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.75835e+03    9.44515e+04   -4.55042e+03   -6.37472e+05    2.91328e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.69483e+02   -5.26453e+05    8.54856e+04   -4.40968e+05   -4.36455e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99065e+02   -2.24597e+02   -8.72545e+01    2.81118e-06
> 
>            Step           Time
>           47000       94.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.49635e+03    3.85588e+03    2.63273e+02    1.85505e+03    2.64864e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.67027e+03    9.47374e+04   -4.56211e+03   -6.35804e+05    2.91047e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.41188e+02   -5.24488e+05    8.68488e+04   -4.37639e+05   -4.36468e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.03834e+02   -2.25751e+02    1.30742e+02    3.02333e-06
> 
>            Step           Time
>           47500       95.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.44465e+03    3.77290e+03    2.70450e+02    1.80800e+03    2.64436e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.78689e+03    9.24139e+04   -4.56883e+03   -6.32750e+05    2.95013e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.25142e+02   -5.23702e+05    8.55553e+04   -4.38147e+05   -4.36476e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99309e+02   -2.26417e+02   -1.73043e+02    2.78673e-06
> 
>            Step           Time
>           48000       96.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.46818e+03    3.83823e+03    2.12252e+02    1.77079e+03    2.71198e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.80566e+03    9.36374e+04   -4.57402e+03   -6.33896e+05    2.88055e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.79889e+02   -5.23665e+05    8.55301e+04   -4.38135e+05   -4.36482e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99221e+02   -2.26931e+02    1.21309e+02    2.76162e-06
> 
>            Step           Time
>           48500       97.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.34091e+03    3.60358e+03    2.40005e+02    1.80901e+03    2.69856e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.78456e+03    9.45658e+04   -4.56261e+03   -6.36481e+05    2.90202e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.72845e+02   -5.25627e+05    8.62328e+04   -4.39394e+05   -4.36516e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01679e+02   -2.25801e+02    2.99517e+02    2.82003e-06
> 
>            Step           Time
>           49000       98.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.60687e+03    3.87281e+03    2.65901e+02    1.81717e+03    2.68240e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.78023e+03    9.37259e+04   -4.58281e+03   -6.34678e+05    3.03099e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     5.26679e+02   -5.23952e+05    8.55931e+04   -4.38359e+05   -4.36467e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99441e+02   -2.27803e+02    1.39649e+02    2.67374e-06
> 
>            Step           Time
>           49500       99.00000
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.43741e+03    3.85808e+03    2.43647e+02    1.85901e+03    2.62149e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69526e+03    9.25260e+04   -4.55909e+03   -6.32522e+05    3.02028e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.99864e+02   -5.23320e+05    8.65864e+04   -4.36734e+05   -4.36506e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.02916e+02   -2.25453e+02   -1.15034e+02    3.16170e-06
> 
>            Step           Time
>           50000      100.00000
> 
> Writing checkpoint, step 50000 at Fri Aug 21 17:31:53 2020
> 
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.43285e+03    3.67909e+03    2.36931e+02    1.77157e+03    2.67285e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.69421e+03    9.32349e+04   -4.56327e+03   -6.34275e+05    2.93845e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.36659e+02   -5.24741e+05    8.56078e+04   -4.39133e+05   -4.36509e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     2.99493e+02   -2.25867e+02   -8.77051e+01    2.70262e-06
> 
> 
> 	<======  ###############  ==>
> 	<====  A V E R A G E S  ====>
> 	<==  ###############  ======>
> 
> 	Statistics over 50001 steps using 501 frames
> 
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>     1.45728e+03    3.74017e+03    2.50095e+02    1.82552e+03    2.66671e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     7.73688e+03    9.34839e+04   -4.56116e+03   -6.34406e+05    2.93995e+03
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     4.72213e+02   -5.24395e+05    8.57743e+04   -4.38620e+05   -4.36434e+05
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.00075e+02   -2.25659e+02   -3.31730e+00    0.00000e+00
> 
>           Box-X          Box-Y          Box-Z
>     6.95233e+00    6.95233e+00    6.95233e+00
> 
>    Total Virial (kJ/mol)
>     2.86095e+04   -1.57443e+02   -1.13729e+02
>    -1.57603e+02    2.86158e+04    1.10600e+02
>    -1.14211e+02    1.10620e+02    2.86547e+04
> 
>    Pressure (bar)
>    -3.83993e-01    1.61303e+01    1.29425e+01
>     1.61461e+01   -3.06741e+00   -1.20991e+01
>     1.29899e+01   -1.21014e+01   -6.50051e+00
> 
>       T-Protein  T-non-Protein
>     3.00021e+02    3.00079e+02
> 
> 
> 	M E G A - F L O P S   A C C O U N T I N G
> 
>  NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
>  RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
>  W3=SPC/TIP3p  W4=TIP4p (single or pairs)
>  V&F=Potential and force  V=Potential only  F=Force only
> 
>  Computing:                               M-Number         M-Flops  % Flops
> -----------------------------------------------------------------------------
>  Pair Search distance check           15120.751268      136086.761     0.2
>  NxN Ewald Elec. + LJ [F]            534341.294592    35266525.443    52.2
>  NxN Ewald Elec. + LJ [V&F]            5407.896848      578644.963     0.9
>  NxN Ewald Elec. [F]                 470672.551296    28711025.629    42.5
>  NxN Ewald Elec. [V&F]                 4764.276400      400199.218     0.6
>  1,4 nonbonded interactions             255.305106       22977.460     0.0
>  Calc Weights                          5081.501628      182934.059     0.3
>  Spread Q Bspline                    108405.368064      216810.736     0.3
>  Gather F Bspline                    108405.368064      650432.208     1.0
>  3D-FFT                              139519.590336     1116156.723     1.7
>  Solve PME                               96.801936        6195.324     0.0
>  Shift-X                                 33.909876         203.459     0.0
>  Bonds                                   51.251025        3023.810     0.0
>  Angles                                 177.353547       29795.396     0.0
>  Propers                                 21.300426        4877.798     0.0
>  RB-Dihedrals                           197.503950       48783.476     0.1
>  Pos. Restr.                             50.051001        2502.550     0.0
>  Virial                                 169.638921        3053.501     0.0
>  Stop-CM                                 16.971876         169.719     0.0
>  Calc-Ekin                              338.827752        9148.349     0.0
>  Lincs                                   47.950959        2877.058     0.0
>  Lincs-Mat                              238.804776         955.219     0.0
>  Constraint-V                          1691.333826       13530.671     0.0
>  Constraint-Vir                         164.367867        3944.829     0.0
>  Settle                                 531.810636      171774.835     0.3
> -----------------------------------------------------------------------------
>  Total                                                67582629.192   100.0
> -----------------------------------------------------------------------------
> 
> 
>      R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
> 
> On 1 MPI rank, each using 4 OpenMP threads
> 
>  Computing:          Num   Num      Call    Wall time         Giga-Cycles
>                      Ranks Threads  Count      (s)         total sum    %
> -----------------------------------------------------------------------------
>  Neighbor search        1    4       1001      12.616        135.936   2.6
>  Force                  1    4      50001     381.839       4114.443  79.3
>  PME mesh               1    4      50001      69.887        753.059  14.5
>  NB X/F buffer ops.     1    4      99001       4.934         53.164   1.0
>  Write traj.            1    4        101       1.946         20.965   0.4
>  Update                 1    4      50001       2.865         30.867   0.6
>  Constraints            1    4      50001       5.418         58.381   1.1
>  Rest                                           1.800         19.396   0.4
> -----------------------------------------------------------------------------
>  Total                                        481.304       5186.212 100.0
> -----------------------------------------------------------------------------
>  Breakdown of PME mesh computation
> -----------------------------------------------------------------------------
>  PME spread             1    4      50001      30.501        328.660   6.3
>  PME gather             1    4      50001      17.960        193.526   3.7
>  PME 3D-FFT             1    4     100002      19.339        208.385   4.0
>  PME solve Elec         1    4      50001       1.981         21.350   0.4
> -----------------------------------------------------------------------------
> 
>                Core t (s)   Wall t (s)        (%)
>        Time:     1924.993      481.304      400.0
>                  (ns/day)    (hour/ns)
> Performance:       17.952        1.337
> Finished mdrun on rank 0 Fri Aug 21 17:31:53 2020

pszilard · September 1, 2020, 9:39am

That confirms that the different cutoffs rvdw = rcoulomb = 1 while the other rvdw = rcoulomb = 1.4.

kw24 · September 2, 2020, 12:29am

Could you explain in layman’s terms why the cutoff variations result in different performances?

pszilard · September 2, 2020, 2:52pm

The larger the cutoff radius, the larger the number of pair interactions that needs to be computed and the larger the computational cost of the short-range non-bonded calculation.

kw24 · September 4, 2020, 7:05pm

Thank you!

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