:-) GROMACS - mdrun_mpi, 2020.4 (-: 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: mdrun_mpi, version 2020.4 Executable: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi Data prefix: /shared/ucl/apps/gromacs/2020.4/intel-2020 Working dir: /lustre/scratch/scratch/ucbechz/Ipsen/20211227_TSI_MD/test_2_xtc/production Process ID: 215539 Command line: mdrun_mpi -v -deffnm md_0_1 -maxh 1 GROMACS version: 2020.4 Verified release checksum is 79c2857291b034542c26e90512b92fd4b184a1c9d6fa59c55f2e24ccf14e7281 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: AVX_512 FFT library: Intel MKL RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icc Intel 19.1.0.20191121 C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG C++ compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icpc Intel 19.1.0.20191121 C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG Running on 1 node with total 36 cores, 36 logical cores Hardware detected on host node-l00a-004.myriad.ucl.ac.uk (the node of MPI rank 0): CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz Family: 6 Model: 85 Stepping: 7 Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Number of AVX-512 FMA units: 2 Hardware topology: Only logical processor count ++++ 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.4054979 -------- -------- --- Thank You --- -------- -------- The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1 Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 1000000000000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -1116166085 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 50000 nstcalcenergy = 100 nstenergy = 50000 nstxout-compressed = 50000 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 = 96 fourier-ny = 96 fourier-nz = 96 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 = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 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 grpopts: nrdf: 31943.7 339423 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 1.105 Initializing Domain Decomposition on 12 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.486 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.447 nm, LJ-14, atoms 14356 15538 multi-body bonded interactions: 0.447 nm, Proper Dih., atoms 14356 15538 Minimum cell size due to bonded interactions: 0.492 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.871 nm Estimated maximum distance required for P-LINCS: 0.871 nm This distance will limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Optimizing the DD grid for 12 cells with a minimum initial size of 1.089 nm The maximum allowed number of cells is: X 10 Y 10 Z 8 Domain decomposition grid 4 x 3 x 1, separate PME ranks 0 PME domain decomposition: 4 x 3 x 1 Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 2.81 nm Y 3.75 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 2.812 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 The minimum size for domain decomposition cells is 1.105 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.39 Y 0.29 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 1.105 nm Using 12 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process 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 1052 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1052 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1052 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 0.105 nm, rlist 1.105 nm inner list: updated every 12 steps, buffer 0.001 nm, rlist 1.001 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 50 steps, buffer 0.231 nm, rlist 1.231 nm inner list: updated every 12 steps, buffer 0.046 nm, rlist 1.046 nm Using Lorentz-Berthelot Lennard-Jones combination rule Long Range LJ corr.: 3.2225e-04 Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 18129 There are constraints between atoms in different decomposition domains, will communicate selected coordinates each lincs iteration ++++ 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 --- -------- -------- Linking all bonded interactions to atoms Intra-simulation communication will occur every 10 steps. ++++ 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: 185570 Atoms Atom distribution over 12 domains: av 15464 stddev 241 min 15216 max 15947 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 Thu Jan 13 11:11:47 2022 Step Time 0 0.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.76530e+04 5.46443e+04 1.92196e+03 1.91126e+04 1.84629e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.26642e+05 -2.51186e+04 -3.16143e+06 1.81425e+04 -2.54380e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62991e+05 -2.08081e+06 -2.08070e+06 2.99892e+02 -2.25929e+02 Pressure (bar) Constr. rmsd -1.00839e+00 2.62777e-05 DD step 49 load imb.: force 14.0% step 150 Turning on dynamic load balancing, because the performance loss due to load imbalance is 8.1 %. DD step 49999 vol min/aver 0.851 load imb.: force 0.4% Step Time 50000 100.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.72392e+04 5.47068e+04 1.90699e+03 1.91703e+04 1.85136e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.29546e+05 -2.51530e+04 -3.17013e+06 1.79943e+04 -2.54958e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.64019e+05 -2.08556e+06 -2.09623e+06 3.00558e+02 -2.26548e+02 Pressure (bar) Constr. rmsd 1.30593e+01 2.66829e-05 Writing checkpoint, step 70100 at Thu Jan 13 11:26:47 2022 DD step 99999 vol min/aver 0.852 load imb.: force 0.3% Step Time 100000 200.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.75152e+04 5.49266e+04 2.01463e+03 1.93423e+04 1.85096e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28542e+05 -2.50609e+04 -3.16412e+06 1.82004e+04 -2.54354e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62641e+05 -2.08090e+06 -2.11143e+06 2.99665e+02 -2.24895e+02 Pressure (bar) Constr. rmsd 2.06828e+01 2.58914e-05 Writing checkpoint, step 140400 at Thu Jan 13 11:41:47 2022 DD step 149999 vol min/aver 0.840 load imb.: force 0.3% Step Time 150000 300.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.75298e+04 5.47227e+04 1.95988e+03 1.92493e+04 1.85379e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.23052e+05 -2.51519e+04 -3.15832e+06 1.78927e+04 -2.54369e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.63060e+05 -2.08063e+06 -2.12681e+06 2.99937e+02 -2.26529e+02 Pressure (bar) Constr. rmsd -1.15041e+02 2.71528e-05 DD step 199999 vol min/aver 0.843 load imb.: force 0.6% Step Time 200000 400.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.76203e+04 5.48318e+04 1.92978e+03 1.92854e+04 1.84959e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28374e+05 -2.51735e+04 -3.16775e+06 1.79555e+04 -2.54797e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.63724e+05 -2.08425e+06 -2.14229e+06 3.00367e+02 -2.26918e+02 Pressure (bar) Constr. rmsd 2.65394e+01 2.64604e-05 Writing checkpoint, step 210300 at Thu Jan 13 11:56:47 2022 DD step 249999 vol min/aver 0.843 load imb.: force 0.4% Step Time 250000 500.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.76882e+04 5.47126e+04 1.92802e+03 1.92349e+04 1.85168e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.29579e+05 -2.51560e+04 -3.16739e+06 1.80271e+04 -2.54621e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.64477e+05 -2.08173e+06 -2.15770e+06 3.00854e+02 -2.26603e+02 Pressure (bar) Constr. rmsd 8.28644e+01 2.68130e-05 Step 277150: Run time exceeded 0.990 hours, will terminate the run within 50 steps Step Time 277200 554.40000 Writing checkpoint, step 277200 at Thu Jan 13 12:11:12 2022 Reading checkpoint file md_0_1.cpt file generated by: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi file generated at: Thu Jan 13 12:11:12 2022 GROMACS double prec.: 0 simulation part #: 1 step: 277200 time: 554.400000 ----------------------------------------------------------- Restarting from checkpoint, appending to previous log file. :-) GROMACS - mdrun_mpi, 2020.4 (-: Executable: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi Data prefix: /shared/ucl/apps/gromacs/2020.4/intel-2020 Working dir: /lustre/scratch/scratch/ucbechz/Ipsen/20211227_TSI_MD/test_2_xtc/production Process ID: 89962 Command line: mdrun_mpi -v -deffnm md_0_1 -cpi -append -maxh 1 GROMACS version: 2020.4 Verified release checksum is 79c2857291b034542c26e90512b92fd4b184a1c9d6fa59c55f2e24ccf14e7281 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: AVX_512 FFT library: Intel MKL RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icc Intel 19.1.0.20191121 C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG C++ compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icpc Intel 19.1.0.20191121 C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG Changing nstlist from 10 to 50, rlist from 1 to 1.105 Initializing Domain Decomposition on 12 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.486 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.440 nm, LJ-14, atoms 14356 15538 multi-body bonded interactions: 0.440 nm, Proper Dih., atoms 14356 15538 Minimum cell size due to bonded interactions: 0.484 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.871 nm Estimated maximum distance required for P-LINCS: 0.871 nm This distance will limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Optimizing the DD grid for 12 cells with a minimum initial size of 1.089 nm The maximum allowed number of cells is: X 10 Y 10 Z 8 Domain decomposition grid 4 x 3 x 1, separate PME ranks 0 PME domain decomposition: 4 x 3 x 1 Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 2.81 nm Y 3.75 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 2.812 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 The minimum size for domain decomposition cells is 1.105 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.39 Y 0.29 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 1.105 nm Using 12 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process 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 1052 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1052 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1052 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 0.105 nm, rlist 1.105 nm inner list: updated every 12 steps, buffer 0.001 nm, rlist 1.001 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 50 steps, buffer 0.231 nm, rlist 1.231 nm inner list: updated every 12 steps, buffer 0.046 nm, rlist 1.046 nm Using Lorentz-Berthelot Lennard-Jones combination rule Long Range LJ corr.: 3.2225e-04 Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 18129 There are constraints between atoms in different decomposition domains, will communicate selected coordinates each lincs iteration ++++ 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 --- -------- -------- Linking all bonded interactions to atoms Intra-simulation communication will occur every 10 steps. There are: 185570 Atoms Atom distribution over 12 domains: av 15464 stddev 238 min 15246 max 16018 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 Thu Jan 13 12:17:59 2022 DD step 277249 load imb.: force 14.3% step 277350 Turning on dynamic load balancing, because the performance loss due to load imbalance is 8.1 %. DD step 299999 vol min/aver 0.847 load imb.: force 0.4% Step Time 300000 600.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.76848e+04 5.48334e+04 1.99660e+03 1.91322e+04 1.85254e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.25874e+05 -2.50865e+04 -3.16349e+06 1.82853e+04 -2.54551e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62884e+05 -2.08263e+06 -2.17303e+06 2.99823e+02 -2.25353e+02 Pressure (bar) Constr. rmsd -1.06289e+02 2.69532e-05 Writing checkpoint, step 330400 at Thu Jan 13 12:32:59 2022 DD step 349999 vol min/aver 0.851 load imb.: force 0.3% Step Time 350000 700.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.70754e+04 5.48432e+04 2.00744e+03 1.91666e+04 1.84902e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.30600e+05 -2.51408e+04 -3.17246e+06 1.78414e+04 -2.55117e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.64344e+05 -2.08682e+06 -2.18853e+06 3.00769e+02 -2.26328e+02 Pressure (bar) Constr. rmsd 2.52728e+01 2.65204e-05 Writing checkpoint, step 384900 at Thu Jan 13 12:48:00 2022 DD step 399999 vol min/aver 0.852 load imb.: force 0.5% Step Time 400000 800.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.75376e+04 5.46735e+04 2.14755e+03 1.93500e+04 1.85192e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.26843e+05 -2.51058e+04 -3.16559e+06 1.78428e+04 -2.54711e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.63236e+05 -2.08388e+06 -2.20390e+06 3.00050e+02 -2.25699e+02 Pressure (bar) Constr. rmsd 1.96505e+01 2.61357e-05 Writing checkpoint, step 439100 at Thu Jan 13 13:03:00 2022 DD step 449999 vol min/aver 0.854 load imb.: force 0.3% Step Time 450000 900.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.75247e+04 5.47687e+04 2.01765e+03 1.92746e+04 1.85175e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.24788e+05 -2.50813e+04 -3.16296e+06 1.79445e+04 -2.54654e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62546e+05 -2.08400e+06 -2.21927e+06 2.99604e+02 -2.25261e+02 Pressure (bar) Constr. rmsd -1.01486e+02 2.61026e-05 Step 491350: Run time exceeded 0.990 hours, will terminate the run within 50 steps Step Time 491400 982.80000 Writing checkpoint, step 491400 at Thu Jan 13 13:17:25 2022 Reading checkpoint file md_0_1.cpt file generated by: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi file generated at: Thu Jan 13 13:17:25 2022 GROMACS double prec.: 0 simulation part #: 2 step: 491400 time: 982.800000 ----------------------------------------------------------- Restarting from checkpoint, appending to previous log file. :-) GROMACS - mdrun_mpi, 2020.4 (-: Executable: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi Data prefix: /shared/ucl/apps/gromacs/2020.4/intel-2020 Working dir: /lustre/scratch/scratch/ucbechz/Ipsen/20211227_TSI_MD/test_2_xtc/production Process ID: 190040 Command line: mdrun_mpi -v -deffnm md_0_1 -cpi -append -maxh 1 GROMACS version: 2020.4 Verified release checksum is 79c2857291b034542c26e90512b92fd4b184a1c9d6fa59c55f2e24ccf14e7281 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: AVX_512 FFT library: Intel MKL RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icc Intel 19.1.0.20191121 C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG C++ compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icpc Intel 19.1.0.20191121 C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG Changing nstlist from 10 to 50, rlist from 1 to 1.105 Initializing Domain Decomposition on 12 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.486 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.445 nm, LJ-14, atoms 14361 15533 multi-body bonded interactions: 0.445 nm, Proper Dih., atoms 15533 14361 Minimum cell size due to bonded interactions: 0.490 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.871 nm Estimated maximum distance required for P-LINCS: 0.871 nm This distance will limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Optimizing the DD grid for 12 cells with a minimum initial size of 1.089 nm The maximum allowed number of cells is: X 10 Y 10 Z 8 Domain decomposition grid 4 x 3 x 1, separate PME ranks 0 PME domain decomposition: 4 x 3 x 1 Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 2.81 nm Y 3.75 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 2.811 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 The minimum size for domain decomposition cells is 1.105 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.39 Y 0.29 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 1.105 nm Using 12 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process 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 1052 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1052 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1052 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 0.105 nm, rlist 1.105 nm inner list: updated every 12 steps, buffer 0.001 nm, rlist 1.001 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 50 steps, buffer 0.231 nm, rlist 1.231 nm inner list: updated every 12 steps, buffer 0.046 nm, rlist 1.046 nm Using Lorentz-Berthelot Lennard-Jones combination rule Long Range LJ corr.: 3.2225e-04 Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 18129 There are constraints between atoms in different decomposition domains, will communicate selected coordinates each lincs iteration ++++ 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 --- -------- -------- Linking all bonded interactions to atoms Intra-simulation communication will occur every 10 steps. There are: 185570 Atoms Atom distribution over 12 domains: av 15464 stddev 255 min 15138 max 15953 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 Thu Jan 13 13:25:37 2022 DD step 491449 load imb.: force 14.2% step 491550 Turning on dynamic load balancing, because the performance loss due to load imbalance is 8.5 %. DD step 499999 vol min/aver 0.853 load imb.: force 0.7% Step Time 500000 1000.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.77155e+04 5.46407e+04 1.92078e+03 1.93440e+04 1.85320e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28158e+05 -2.51248e+04 -3.16869e+06 1.80546e+04 -2.54866e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62637e+05 -2.08602e+06 -2.23470e+06 2.99663e+02 -2.26041e+02 Pressure (bar) Constr. rmsd 1.32554e+01 2.60255e-05 DD step 549999 vol min/aver 0.856 load imb.: force 0.4% Step Time 550000 1100.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.76817e+04 5.47208e+04 2.01841e+03 1.91074e+04 1.85074e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28165e+05 -2.51334e+04 -3.16633e+06 1.78811e+04 -2.54681e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.64737e+05 -2.08208e+06 -2.25009e+06 3.01023e+02 -2.26196e+02 Pressure (bar) Constr. rmsd -3.65888e+01 2.67560e-05 Writing checkpoint, step 556200 at Thu Jan 13 13:40:38 2022 DD step 599999 vol min/aver 0.839 load imb.: force 0.4% Step Time 600000 1200.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.75243e+04 5.47401e+04 2.01254e+03 1.91454e+04 1.85104e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28278e+05 -2.51142e+04 -3.16749e+06 1.78643e+04 -2.54793e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.61902e+05 -2.08603e+06 -2.26550e+06 2.99187e+02 -2.25851e+02 Pressure (bar) Constr. rmsd 2.32733e+01 2.65952e-05 Writing checkpoint, step 621100 at Thu Jan 13 13:55:38 2022 DD step 649999 vol min/aver 0.857 load imb.: force 0.8% Step Time 650000 1300.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.73022e+04 5.44163e+04 1.98070e+03 1.92461e+04 1.85321e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.29413e+05 -2.51584e+04 -3.16891e+06 1.81652e+04 -2.54822e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.63234e+05 -2.08499e+06 -2.28095e+06 3.00050e+02 -2.26645e+02 Pressure (bar) Constr. rmsd 1.62660e+02 2.61863e-05 Writing checkpoint, step 685900 at Thu Jan 13 14:10:38 2022 DD step 699999 vol min/aver 0.845 load imb.: force 0.5% Step Time 700000 1400.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.73646e+04 5.44676e+04 1.96257e+03 1.91440e+04 1.85276e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.30094e+05 -2.51330e+04 -3.16928e+06 1.80888e+04 -2.54802e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.64140e+05 -2.08388e+06 -2.29637e+06 3.00636e+02 -2.26189e+02 Pressure (bar) Constr. rmsd 3.03620e+01 2.65291e-05 Step 748000: Run time exceeded 0.990 hours, will terminate the run within 50 steps Step Time 748050 1496.10000 Writing checkpoint, step 748050 at Thu Jan 13 14:25:02 2022 Reading checkpoint file md_0_1.cpt file generated by: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi file generated at: Thu Jan 13 14:25:02 2022 GROMACS double prec.: 0 simulation part #: 3 step: 748050 time: 1496.100000 ----------------------------------------------------------- Restarting from checkpoint, appending to previous log file. :-) GROMACS - mdrun_mpi, 2020.4 (-: Executable: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi Data prefix: /shared/ucl/apps/gromacs/2020.4/intel-2020 Working dir: /lustre/scratch/scratch/ucbechz/Ipsen/20211227_TSI_MD/test_2_xtc/production Process ID: 168838 Command line: mdrun_mpi -v -deffnm md_0_1 -cpi -append -maxh 1 GROMACS version: 2020.4 Verified release checksum is 79c2857291b034542c26e90512b92fd4b184a1c9d6fa59c55f2e24ccf14e7281 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: AVX_512 FFT library: Intel MKL RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icc Intel 19.1.0.20191121 C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG C++ compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icpc Intel 19.1.0.20191121 C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG Changing nstlist from 10 to 50, rlist from 1 to 1.105 Initializing Domain Decomposition on 12 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.486 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.442 nm, LJ-14, atoms 14361 15533 multi-body bonded interactions: 0.442 nm, Proper Dih., atoms 15533 14361 Minimum cell size due to bonded interactions: 0.486 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.871 nm Estimated maximum distance required for P-LINCS: 0.871 nm This distance will limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Optimizing the DD grid for 12 cells with a minimum initial size of 1.089 nm The maximum allowed number of cells is: X 10 Y 10 Z 8 Domain decomposition grid 4 x 3 x 1, separate PME ranks 0 PME domain decomposition: 4 x 3 x 1 Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 2.81 nm Y 3.75 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 2.813 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 The minimum size for domain decomposition cells is 1.105 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.39 Y 0.29 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 1.105 nm Using 12 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process 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 1052 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1052 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1052 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 0.105 nm, rlist 1.105 nm inner list: updated every 12 steps, buffer 0.001 nm, rlist 1.001 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 50 steps, buffer 0.231 nm, rlist 1.231 nm inner list: updated every 12 steps, buffer 0.046 nm, rlist 1.046 nm Using Lorentz-Berthelot Lennard-Jones combination rule Long Range LJ corr.: 3.2225e-04 Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 18129 There are constraints between atoms in different decomposition domains, will communicate selected coordinates each lincs iteration ++++ 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 --- -------- -------- Linking all bonded interactions to atoms Intra-simulation communication will occur every 10 steps. There are: 185570 Atoms Atom distribution over 12 domains: av 15464 stddev 234 min 15191 max 15941 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 Thu Jan 13 14:33:55 2022 DD step 748099 load imb.: force 31.6% step 748200 Turning on dynamic load balancing, because the performance loss due to load imbalance is 2.8 %. DD step 749999 vol min/aver 0.700 load imb.: force 39.3% Step Time 750000 1500.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.68955e+04 5.46092e+04 2.03788e+03 1.92568e+04 1.84984e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.27456e+05 -2.51463e+04 -3.16521e+06 1.80780e+04 -2.54704e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62562e+05 -2.08447e+06 -2.31183e+06 2.99614e+02 -2.26427e+02 Pressure (bar) Constr. rmsd 3.79740e+01 2.66395e-05 Writing checkpoint, step 754550 at Thu Jan 13 14:49:03 2022 Writing checkpoint, step 760950 at Thu Jan 13 15:04:02 2022 step 767050 Turning off dynamic load balancing, because it is degrading performance. Atom distribution over 12 domains: av 15464 stddev 238 min 15218 max 15942 Writing checkpoint, step 767250 at Thu Jan 13 15:18:58 2022 step 773050 Turning on dynamic load balancing, because the performance loss due to load imbalance is 5.6 %. step 774050 Turning off dynamic load balancing, because it is degrading performance. Atom distribution over 12 domains: av 15464 stddev 249 min 15209 max 16026 Step 774300: Run time exceeded 0.990 hours, will terminate the run within 50 steps Step Time 774350 1548.70000 Writing checkpoint, step 774350 at Thu Jan 13 15:33:29 2022 Reading checkpoint file md_0_1.cpt file generated by: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi file generated at: Thu Jan 13 15:33:29 2022 GROMACS double prec.: 0 simulation part #: 4 step: 774350 time: 1548.700000 ----------------------------------------------------------- Restarting from checkpoint, appending to previous log file. :-) GROMACS - mdrun_mpi, 2020.4 (-: Executable: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi Data prefix: /shared/ucl/apps/gromacs/2020.4/intel-2020 Working dir: /lustre/scratch/scratch/ucbechz/Ipsen/20211227_TSI_MD/test_2_xtc/production Process ID: 82463 Command line: mdrun_mpi -v -deffnm md_0_1 -cpi -append -maxh 1 GROMACS version: 2020.4 Verified release checksum is 79c2857291b034542c26e90512b92fd4b184a1c9d6fa59c55f2e24ccf14e7281 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: AVX_512 FFT library: Intel MKL RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icc Intel 19.1.0.20191121 C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG C++ compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icpc Intel 19.1.0.20191121 C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG Changing nstlist from 10 to 50, rlist from 1 to 1.105 Initializing Domain Decomposition on 12 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.486 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.457 nm, LJ-14, atoms 14361 15533 multi-body bonded interactions: 0.457 nm, Proper Dih., atoms 15533 14361 Minimum cell size due to bonded interactions: 0.503 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.871 nm Estimated maximum distance required for P-LINCS: 0.871 nm This distance will limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Optimizing the DD grid for 12 cells with a minimum initial size of 1.089 nm The maximum allowed number of cells is: X 10 Y 10 Z 8 Domain decomposition grid 4 x 3 x 1, separate PME ranks 0 PME domain decomposition: 4 x 3 x 1 Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 2.81 nm Y 3.75 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 2.812 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 The minimum size for domain decomposition cells is 1.105 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.39 Y 0.29 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 1.105 nm Using 12 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process 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 1052 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1052 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1052 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 0.105 nm, rlist 1.105 nm inner list: updated every 12 steps, buffer 0.001 nm, rlist 1.001 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 50 steps, buffer 0.231 nm, rlist 1.231 nm inner list: updated every 12 steps, buffer 0.046 nm, rlist 1.046 nm Using Lorentz-Berthelot Lennard-Jones combination rule Long Range LJ corr.: 3.2225e-04 Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 18129 There are constraints between atoms in different decomposition domains, will communicate selected coordinates each lincs iteration ++++ 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 --- -------- -------- Linking all bonded interactions to atoms Intra-simulation communication will occur every 10 steps. There are: 185570 Atoms Atom distribution over 12 domains: av 15464 stddev 239 min 15154 max 15955 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 Thu Jan 13 15:37:56 2022 DD step 774399 load imb.: force 15.5% step 774500 Turning on dynamic load balancing, because the performance loss due to load imbalance is 9.3 %. DD step 799999 vol min/aver 0.824 load imb.: force 0.6% Step Time 800000 1600.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.75364e+04 5.45087e+04 1.91654e+03 1.92478e+04 1.85350e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.27492e+05 -2.51478e+04 -3.16575e+06 1.79164e+04 -2.54693e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62015e+05 -2.08492e+06 -2.32720e+06 2.99260e+02 -2.26455e+02 Pressure (bar) Constr. rmsd 3.56073e+01 2.60246e-05 Writing checkpoint, step 844400 at Thu Jan 13 15:52:57 2022 DD step 849999 vol min/aver 0.826 load imb.: force 0.4% Step Time 850000 1700.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.78894e+04 5.47200e+04 2.01918e+03 1.89128e+04 1.85778e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.29354e+05 -2.51689e+04 -3.16950e+06 1.80505e+04 -2.54794e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62642e+05 -2.08530e+06 -2.34263e+06 2.99666e+02 -2.26834e+02 Pressure (bar) Constr. rmsd 3.56104e+01 2.62481e-05 DD step 899999 vol min/aver 0.833 load imb.: force 0.4% Step Time 900000 1800.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.77568e+04 5.44922e+04 1.95922e+03 1.91673e+04 1.84980e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.26681e+05 -2.50720e+04 -3.16499e+06 1.80788e+04 -2.54695e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62520e+05 -2.08443e+06 -2.35809e+06 2.99587e+02 -2.25094e+02 Pressure (bar) Constr. rmsd -8.35347e+01 2.71908e-05 Writing checkpoint, step 914400 at Thu Jan 13 16:07:57 2022 DD step 949999 vol min/aver 0.822 load imb.: force 0.2% Step Time 950000 1900.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.72555e+04 5.46949e+04 1.96127e+03 1.90837e+04 1.85393e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.26022e+05 -2.51539e+04 -3.16426e+06 1.79884e+04 -2.54702e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62640e+05 -2.08438e+06 -2.37356e+06 2.99665e+02 -2.26564e+02 Pressure (bar) Constr. rmsd -7.68311e+00 2.58233e-05 Writing checkpoint, step 984200 at Thu Jan 13 16:22:57 2022 DD step 999999 vol min/aver 0.815 load imb.: force 0.4% Step Time 1000000 2000.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.71031e+04 5.47502e+04 2.00819e+03 1.91781e+04 1.85856e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.29231e+05 -2.50798e+04 -3.16788e+06 1.79082e+04 -2.54692e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.62303e+05 -2.08462e+06 -2.38898e+06 2.99447e+02 -2.25234e+02 Pressure (bar) Constr. rmsd 4.32122e+01 2.62177e-05 DD step 1049999 vol min/aver 0.825 load imb.: force 0.4% Step Time 1050000 2100.00000 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.73088e+04 5.48251e+04 1.95527e+03 1.93048e+04 1.85298e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.26460e+05 -2.50904e+04 -3.16628e+06 1.79262e+04 -2.54829e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.63558e+05 -2.08474e+06 -2.40434e+06 3.00259e+02 -2.25424e+02 Pressure (bar) Constr. rmsd -2.03705e-01 2.54587e-05 Step 1051000: Run time exceeded 0.990 hours, will terminate the run within 50 steps Step Time 1051050 2102.10000 Writing checkpoint, step 1051050 at Thu Jan 13 16:37:21 2022 Reading checkpoint file md_0_1.cpt file generated by: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi file generated at: Thu Jan 13 16:37:21 2022 GROMACS double prec.: 0 simulation part #: 5 step: 1051050 time: 2102.100000 ----------------------------------------------------------- Restarting from checkpoint, appending to previous log file. :-) GROMACS - mdrun_mpi, 2020.4 (-: Executable: /shared/ucl/apps/gromacs/2020.4/intel-2020/bin/mdrun_mpi Data prefix: /shared/ucl/apps/gromacs/2020.4/intel-2020 Working dir: /lustre/scratch/scratch/ucbechz/Ipsen/20211227_TSI_MD/test_2_xtc/production Process ID: 8839 Command line: mdrun_mpi -v -deffnm md_0_1 -cpi -append -maxh 1 GROMACS version: 2020.4 Verified release checksum is 79c2857291b034542c26e90512b92fd4b184a1c9d6fa59c55f2e24ccf14e7281 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: AVX_512 FFT library: Intel MKL RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icc Intel 19.1.0.20191121 C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG C++ compiler: /shared/ucl/apps/intel/2020/compilers_and_libraries_2020.0.166/linux/bin/intel64/icpc Intel 19.1.0.20191121 C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG Changing nstlist from 10 to 50, rlist from 1 to 1.105 Initializing Domain Decomposition on 12 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.486 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.447 nm, LJ-14, atoms 14356 15538 multi-body bonded interactions: 0.447 nm, Proper Dih., atoms 14356 15538 Minimum cell size due to bonded interactions: 0.492 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.871 nm Estimated maximum distance required for P-LINCS: 0.871 nm This distance will limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Optimizing the DD grid for 12 cells with a minimum initial size of 1.089 nm The maximum allowed number of cells is: X 10 Y 10 Z 8 Domain decomposition grid 4 x 3 x 1, separate PME ranks 0 PME domain decomposition: 4 x 3 x 1 Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 2.81 nm Y 3.75 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 2.812 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 The minimum size for domain decomposition cells is 1.105 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.39 Y 0.29 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.105 nm two-body bonded interactions (-rdd) 1.105 nm multi-body bonded interactions (-rdd) 1.105 nm atoms separated by up to 5 constraints (-rcon) 1.105 nm Using 12 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process 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 1052 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1052 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1052 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 0.105 nm, rlist 1.105 nm inner list: updated every 12 steps, buffer 0.001 nm, rlist 1.001 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 50 steps, buffer 0.231 nm, rlist 1.231 nm inner list: updated every 12 steps, buffer 0.046 nm, rlist 1.046 nm Using Lorentz-Berthelot Lennard-Jones combination rule Long Range LJ corr.: 3.2225e-04 Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 18129 There are constraints between atoms in different decomposition domains, will communicate selected coordinates each lincs iteration ++++ 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 --- -------- -------- Linking all bonded interactions to atoms Intra-simulation communication will occur every 10 steps. There are: 185570 Atoms Atom distribution over 12 domains: av 15464 stddev 236 min 15222 max 15926 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 Thu Jan 13 16:41:26 2022 DD step 1051099 load imb.: force 7.4% step 1056050 Turning on dynamic load balancing, because the performance loss due to load imbalance is 2.3 %. Writing checkpoint, step 1057050 at Thu Jan 13 16:56:32 2022 ---------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 42783.340 3565.279 1200.0 59:25 (ns/day) (hour/ns) Performance: 13.411 1.790 Finished mdrun on rank 0 Thu Jan 13 16:37:21 2022 step 1062050 Turning off dynamic load balancing, because it is degrading performance. Atom distribution over 12 domains: av 15464 stddev 246 min 15197 max 15962 Writing checkpoint, step 1063200 at Thu Jan 13 17:11:32 2022 step 1066050 Turning on dynamic load balancing, because the performance loss due to load imbalance is 4.0 %. step 1068050 Turning off dynamic load balancing, because it is degrading performance. Atom distribution over 12 domains: av 15464 stddev 247 min 15179 max 15963 Writing checkpoint, step 1069000 at Thu Jan 13 17:26:29 2022 Step 1075100: Run time exceeded 0.990 hours, will terminate the run within 50 steps Step Time 1075150 2150.30000 Writing checkpoint, step 1075150 at Thu Jan 13 17:40:56 2022 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.76405e+04 5.47964e+04 2.03660e+03 1.90495e+04 1.84826e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28534e+05 -2.51019e+04 -3.16718e+06 1.81374e+04 -2.54726e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.61432e+05 -2.08583e+06 -2.41203e+06 2.98882e+02 -2.25629e+02 Pressure (bar) Constr. rmsd -1.85699e+01 2.63710e-05 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 1075151 steps using 10752 frames Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 3.74716e+04 5.47480e+04 1.99394e+03 1.91755e+04 1.85266e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.27550e+05 -2.51208e+04 -3.16603e+06 1.80215e+04 -2.54692e+06 Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) 4.63151e+05 -2.08377e+06 -2.24633e+06 2.99996e+02 -2.25970e+02 Pressure (bar) Constr. rmsd 1.02127e+00 0.00000e+00 Box-X Box-Y Box-Z 1.37749e+01 1.37749e+01 9.74032e+00 Total Virial (kJ/mol) 1.54330e+05 -1.70376e+01 -4.29953e+01 -1.82384e+01 1.54320e+05 2.32806e+02 -4.39624e+01 2.33242e+02 1.54336e+05 Pressure (bar) 1.01163e+00 2.23978e-01 -4.62685e-01 2.45570e-01 -7.74511e-02 -1.35786e+00 -4.45318e-01 -1.36570e+00 2.12960e+00 T-Protein T-non-Protein 2.99895e+02 3.00006e+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 41189.740358 370707.663 0.2 NxN Ewald Elec. + LJ [F] 1531121.335216 101054008.124 53.4 NxN Ewald Elec. + LJ [V&F] 15530.139136 1661724.888 0.9 NxN Ewald Elec. [F] 1220772.769104 74467138.915 39.3 NxN Ewald Elec. [V&F] 12381.758848 1040067.743 0.5 1,4 nonbonded interactions 1142.676612 102840.895 0.1 Calc Weights 13417.267710 483021.638 0.3 Spread Q Bspline 286235.044480 572470.089 0.3 Gather F Bspline 286235.044480 1717410.267 0.9 3D-FFT 842467.807720 6739742.462 3.6 Solve PME 666.344448 42646.045 0.0 Reset In Box 89.073600 267.221 0.0 CG-CoM 89.630310 268.891 0.0 Angles 794.031546 133397.300 0.1 Propers 1406.269249 322035.658 0.2 Impropers 79.653805 16567.991 0.0 Virial 448.711210 8076.802 0.0 Stop-CM 44.722370 447.224 0.0 Calc-Ekin 894.818540 24160.101 0.0 Lincs 601.155615 36069.337 0.0 Lincs-Mat 13015.944792 52063.779 0.0 Constraint-V 5445.688797 43565.510 0.0 Constraint-Vir 484.633932 11631.214 0.0 Settle 1414.459189 456870.318 0.2 ----------------------------------------------------------------------------- Total 189357200.074 100.0 ----------------------------------------------------------------------------- D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 153228.1 av. #atoms communicated per step for LINCS: 2 x 16132.4 Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 33.5%. The balanceable part of the MD step is 13%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 4.3%. 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 12 MPI ranks Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Domain decomp. 12 1 482 53.659 1670.164 1.5 DD comm. load 12 1 325 0.777 24.172 0.0 DD comm. bounds 12 1 160 2.460 76.582 0.1 Neighbor search 12 1 483 20.178 628.060 0.6 Comm. coord. 12 1 23618 172.021 5354.273 4.8 Force 12 1 24101 222.052 6911.522 6.2 Wait + Comm. F 12 1 24101 157.654 4907.105 4.4 PME mesh 12 1 24101 2298.174 71532.284 64.4 NB X/F buffer ops. 12 1 71337 5.143 160.068 0.1 Write traj. 12 1 4 0.410 12.775 0.0 Update 12 1 24101 3.065 95.409 0.1 Constraints 12 1 24101 582.954 18144.857 16.3 Comm. energies 12 1 2411 51.612 1606.464 1.4 Rest 1.128 35.110 0.0 ----------------------------------------------------------------------------- Total 3571.288 111158.846 100.0 ----------------------------------------------------------------------------- Breakdown of PME mesh computation ----------------------------------------------------------------------------- PME redist. X/F 12 1 48202 1184.118 36856.489 33.2 PME spread 12 1 24101 247.938 7717.252 6.9 PME gather 12 1 24101 139.627 4345.982 3.9 PME 3D-FFT 12 1 48202 16.633 517.711 0.5 PME 3D-FFT Comm. 12 1 96404 708.321 22046.989 19.8 PME solve Elec 12 1 24101 1.417 44.095 0.0 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 42854.375 3571.288 1200.0 59:31 (ns/day) (hour/ns) Performance: 1.166 20.581 Finished mdrun on rank 0 Thu Jan 13 17:40:57 2022