:-) GROMACS - gmx mdrun, 2023.1 (-: Copyright 1991-2023 The GROMACS Authors. 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. Current GROMACS contributors: Mark Abraham Andrey Alekseenko Cathrine Bergh Christian Blau Eliane Briand Mahesh Doijade Stefan Fleischmann Vytas Gapsys Gaurav Garg Sergey Gorelov Gilles Gouaillardet Alan Gray M. Eric Irrgang Farzaneh Jalalypour Joe Jordan Christoph Junghans Prashanth Kanduri Sebastian Keller Carsten Kutzner Justin A. Lemkul Magnus Lundborg Pascal Merz Vedran Miletic Dmitry Morozov Szilard Pall Roland Schulz Michael Shirts Alexey Shvetsov Balint Soproni David van der Spoel Philip Turner Carsten Uphoff Alessandra Villa Sebastian Wingbermuehle Artem Zhmurov Previous GROMACS contributors: Emile Apol Rossen Apostolov James Barnett Herman J.C. Berendsen Par Bjelkmar Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Carlo Camilloni Rudi van Drunen Anton Feenstra Oliver Fleetwood Gerrit Groenhof Bert de Groot Anca Hamuraru Vincent Hindriksen Victor Holanda Aleksei Iupinov Dimitrios Karkoulis Peter Kasson Sebastian Kehl Jiri Kraus Per Larsson Viveca Lindahl Erik Marklund Pieter Meulenhoff Teemu Murtola Sander Pronk Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Coordinated by the GROMACS project leaders: Paul Bauer, Berk Hess, and Erik Lindahl GROMACS: gmx mdrun, version 2023.1 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /media/icaspell/01D8D4A7A188BE70/onechain_BIOVIA_Amberff14/gromacs Process ID: 323781 Command line: gmx mdrun -v -deffnm step5_5 GROMACS version: 2023.1 Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128) GPU support: SYCL (hipSYCL) NB cluster size: 8 SIMD instructions: AVX2_256 CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128 GPU FFT library: VkFFT internal (1.2.26-b15cb0ca3e884bdb6c901a12d87aa8aadf7637d8) with HIP backend Multi-GPU FFT: none RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /opt/rocm-5.4.3/llvm/bin/clang Clang 15.0.0 C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG C++ compiler: /opt/rocm-5.4.3/llvm/bin/clang++ Clang 15.0.0 C++ compiler flags: -mavx2 -mfma -Wno-reserved-identifier -Wno-missing-field-initializers -Weverything -Wno-c++98-compat -Wno-c++98-compat-pedantic -Wno-source-uses-openmp -Wno-c++17-extensions -Wno-documentation-unknown-command -Wno-covered-switch-default -Wno-switch-enum -Wno-extra-semi-stmt -Wno-weak-vtables -Wno-shadow -Wno-padded -Wno-reserved-id-macro -Wno-double-promotion -Wno-exit-time-destructors -Wno-global-constructors -Wno-documentation -Wno-format-nonliteral -Wno-used-but-marked-unused -Wno-float-equal -Wno-cuda-compat -Wno-conditional-uninitialized -Wno-conversion -Wno-disabled-macro-expansion -Wno-unused-macros -Wno-unused-parameter -Wno-unused-variable -Wno-newline-eof -Wno-old-style-cast -Wno-zero-as-null-pointer-constant -Wno-unused-but-set-variable -Wno-sign-compare -Wno-unused-result -fopenmp=libomp -O3 -DNDEBUG BLAS library: Internal LAPACK library: Internal hipSYCL launcher: /usr/local/lib/cmake/hipSYCL/syclcc-launcher hipSYCL flags: -Wno-unknown-cuda-version -Wno-unknown-attributes --hipsycl-targets="hip:gfx90c,gfx1032" hipSYCL GPU flags: -ffast-math;-fgpu-inline-threshold=99999 hipSYCL targets: hip:gfx90c,gfx1032 hipSYCL version: hipSYCL 0.9.4-git Running on 1 node with total 6 cores, 12 processing units, 1 compatible GPU Hardware detected on host icaspell-B450M-S2H-V2: CPU info: Vendor: AMD Brand: AMD Ryzen 5 PRO 4650G with Radeon Graphics Family: 23 Model: 96 Stepping: 1 Features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 Hardware topology: Basic Packages, cores, and logical processors: [indices refer to OS logical processors] Package 0: [ 0 6] [ 1 7] [ 2 8] [ 3 9] [ 4 10] [ 5 11] CPU limit set by OS: -1 Recommended max number of threads: 12 GPU info: Number of GPUs detected: 1 #0: name: , architecture 10.3.2, vendor: AMD, device version: 1.2 hipSYCL 0.9.4-git, driver version 50422804, status: compatible ++++ 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.7852175 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 5000000 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 1601892071 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 50000 nstfout = 50000 nstlog = 1000 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 50000 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 20 pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 0.933 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 0.9 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = None rvdw-switch = 0 rvdw = 0.9 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 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 = 3d epsilon-surface = 0 ensemble-temperature-setting = constant ensemble-temperature = 310 tcoupl = Nose-Hoover nsttcouple = 25 nh-chain-length = 1 print-nose-hoover-chain-variables = false pcoupl = Parrinello-Rahman pcoupltype = Isotropic nstpcouple = 100 tau-p = 5 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 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 shift-vector = transformation-matrix = qmmm-cp2k: active = false qmgroup = System qmmethod = PBE qmfilenames = qmcharge = 0 qmmultiplicity = 1 grpopts: nrdf: 12158 195795 ref-t: 310 310 tau-t: 1 1 annealing: No No annealing-npoints: 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Changing nstlist from 20 to 80, rlist from 0.933 to 1.044 When checking whether update groups are usable: Domain decomposition is not active, so there is no need for update groups Update task can not run on the GPU, because the following condition(s) were not satisfied: Nose-Hoover temperature coupling is not supported. NOTE: SYCL GPU support in GROMACS, and the compilers, libraries, and drivers that it depends on are fairly new. Please, pay extra attention to the correctness of your results, and update to the latest GROMACS patch version if warranted. 1 GPU selected for this run. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node: PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU PME tasks will do all aspects on the GPU Using 1 MPI thread Using 12 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 0.288146 nm for Ewald Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Ewald -1.111e-05 Initialized non-bonded Coulomb Ewald tables, spacing: 8.85e-04 size: 1018 Generated table with 1022 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1022 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1022 data points for 1-4 LJ12. Tabscale = 500 points/nm Long Range LJ corr.: 2.9965e-04 Using GPU 8x8 nonbonded short-range kernels Using a dual 8x8 pair-list setup updated with dynamic, rolling pruning: outer list: updated every 80 steps, buffer 0.144 nm, rlist 1.044 nm inner list: updated every 10 steps, buffer 0.003 nm, rlist 0.903 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 80 steps, buffer 0.283 nm, rlist 1.183 nm inner list: updated every 10 steps, buffer 0.044 nm, rlist 0.944 nm Using Lorentz-Berthelot Lennard-Jones combination rule Pinning threads with an auto-selected logical cpu stride of 1 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 2425 ++++ 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 --- -------- -------- There are: 102669 Atoms Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: SOLU 1: SOLV Started mdrun on rank 0 Sat May 20 13:36:12 2023 Step Time 0 0.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 4.05291e+03 1.06818e+04 1.62841e+04 6.90285e+02 4.73116e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.87935e+04 1.91576e+05 -8.73705e+03 -1.67318e+06 1.45697e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.40054e+06 2.68123e+05 -1.13241e+06 -1.13235e+06 3.10145e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.79370e+02 6.81088e+01 3.52918e-06 Step Time 1000 2.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.98543e+03 1.06892e+04 1.62192e+04 6.37280e+02 4.59032e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.85639e+04 1.93445e+05 -8.72596e+03 -1.67321e+06 1.47335e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39907e+06 2.67458e+05 -1.13161e+06 -1.13244e+06 3.09375e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.78661e+02 1.58946e+02 3.42376e-06 step 1680: timed with pme grid 96 96 96, coulomb cutoff 0.900: 941.5 M-cycles step 1840: timed with pme grid 80 80 80, coulomb cutoff 0.949: 883.1 M-cycles step 2000: timed with pme grid 72 72 72, coulomb cutoff 1.055: 1016.1 M-cycles Step Time 2000 4.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.95803e+03 1.07852e+04 1.62530e+04 6.69212e+02 4.61024e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.85567e+04 1.91399e+05 -8.70090e+03 -1.66958e+06 1.19364e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.40011e+06 2.65989e+05 -1.13412e+06 -1.13241e+06 3.07677e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.77063e+02 1.28268e+00 3.33384e-06 step 2160: timed with pme grid 80 80 80, coulomb cutoff 0.949: 879.0 M-cycles step 2320: timed with pme grid 84 84 84, coulomb cutoff 0.904: 971.1 M-cycles step 2480: timed with pme grid 96 96 96, coulomb cutoff 0.900: 876.7 M-cycles step 2640: timed with pme grid 80 80 80, coulomb cutoff 0.949: 871.2 M-cycles step 2800: timed with pme grid 84 84 84, coulomb cutoff 0.904: 872.0 M-cycles step 2960: timed with pme grid 96 96 96, coulomb cutoff 0.900: 883.3 M-cycles Step Time 3000 6.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 4.00850e+03 1.07768e+04 1.61090e+04 5.87112e+02 4.59360e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.86451e+04 1.90517e+05 -8.72054e+03 -1.66924e+06 1.18671e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.40085e+06 2.67780e+05 -1.13307e+06 -1.13241e+06 3.09748e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.78316e+02 -8.06457e+01 3.49252e-06 step 3120: timed with pme grid 80 80 80, coulomb cutoff 0.949: 876.1 M-cycles step 3280: timed with pme grid 84 84 84, coulomb cutoff 0.904: 877.8 M-cycles step 3440: timed with pme grid 96 96 96, coulomb cutoff 0.900: 894.0 M-cycles optimal pme grid 80 80 80, coulomb cutoff 0.949 Step Time 4000 8.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.96345e+03 1.08978e+04 1.62404e+04 5.25364e+02 4.56149e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.86188e+04 1.90992e+05 -8.69042e+03 -1.66830e+06 1.20264e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39916e+06 2.68856e+05 -1.13031e+06 -1.13233e+06 3.10993e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.76396e+02 -8.94044e+01 3.36738e-06 Step Time 5000 10.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 4.01877e+03 1.06260e+04 1.60909e+04 5.86432e+02 4.64369e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.86647e+04 1.90134e+05 -8.74806e+03 -1.66963e+06 1.20109e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.40160e+06 2.66002e+05 -1.13560e+06 -1.13231e+06 3.07691e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.80075e+02 -1.78808e+01 3.34430e-06 Step Time 6000 12.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.85286e+03 1.03437e+04 1.60946e+04 6.23398e+02 4.60694e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.87005e+04 1.90299e+05 -8.68467e+03 -1.66721e+06 1.21204e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39925e+06 2.67537e+05 -1.13172e+06 -1.13213e+06 3.09468e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.76030e+02 -1.14875e+02 3.43142e-06 Step Time 7000 14.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.90905e+03 1.05681e+04 1.62195e+04 6.19302e+02 4.74429e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.86725e+04 1.91285e+05 -8.72374e+03 -1.66611e+06 1.17833e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39703e+06 2.67422e+05 -1.12961e+06 -1.13205e+06 3.09334e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.78520e+02 1.47534e+02 3.26195e-06 Step Time 8000 16.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.88368e+03 1.05513e+04 1.62325e+04 6.22251e+02 4.64770e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.87493e+04 1.91679e+05 -8.72014e+03 -1.66724e+06 1.20307e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39757e+06 2.68187e+05 -1.12938e+06 -1.13226e+06 3.10219e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.78290e+02 2.66325e+01 3.24815e-06 Step Time 9000 18.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.85180e+03 1.06696e+04 1.61696e+04 5.60502e+02 4.69911e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.85442e+04 1.89762e+05 -8.67215e+03 -1.66545e+06 1.20695e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39780e+06 2.68009e+05 -1.12979e+06 -1.13230e+06 3.10013e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.75235e+02 -1.09543e+02 3.24898e-06 Step Time 10000 20.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.90682e+03 1.06608e+04 1.63173e+04 6.19872e+02 4.75813e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.88426e+04 1.90736e+05 -8.72762e+03 -1.67037e+06 1.17167e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.40154e+06 2.67217e+05 -1.13432e+06 -1.13256e+06 3.09097e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.78768e+02 1.16784e+00 3.19174e-06 Step Time 11000 22.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 4.06565e+03 1.08892e+04 1.62681e+04 5.88022e+02 4.68916e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.87105e+04 1.89543e+05 -8.70703e+03 -1.66455e+06 1.18860e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39662e+06 2.68893e+05 -1.12773e+06 -1.13176e+06 3.11036e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.77454e+02 -6.06591e+01 3.29245e-06 Step Time 12000 24.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 4.07610e+03 1.10274e+04 1.62535e+04 5.60467e+02 4.62163e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.87042e+04 1.91333e+05 -8.70920e+03 -1.66863e+06 1.19783e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39879e+06 2.67176e+05 -1.13161e+06 -1.13220e+06 3.09050e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.77592e+02 -8.77351e-01 3.39090e-06 Step Time 13000 26.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 4.08469e+03 1.09225e+04 1.60699e+04 5.92669e+02 4.70653e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.87382e+04 1.88925e+05 -8.71610e+03 -1.66432e+06 1.19167e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39708e+06 2.69626e+05 -1.12746e+06 -1.13211e+06 3.11884e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.78032e+02 1.89955e+01 3.37978e-06 Step Time 14000 28.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.86801e+03 1.07753e+04 1.60820e+04 5.33658e+02 4.60472e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.90052e+04 1.92351e+05 -8.70596e+03 -1.66815e+06 1.19731e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39766e+06 2.70088e+05 -1.12758e+06 -1.13231e+06 3.12418e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.77386e+02 1.18007e+02 3.40997e-06 Step Time 15000 30.00000 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.96121e+03 1.07963e+04 1.62692e+04 6.36611e+02 4.66389e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.88119e+04 1.89900e+05 -8.69696e+03 -1.66571e+06 1.18673e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39750e+06 2.70070e+05 -1.12743e+06 -1.13192e+06 3.12397e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.76812e+02 -8.71136e+01 3.23796e-06 Received the INT signal, stopping within 80 steps Step Time 15520 31.04000 Writing checkpoint, step 15520 at Sat May 20 13:37:28 2023 Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 4.00101e+03 1.08423e+04 1.62725e+04 6.24639e+02 4.68485e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.85362e+04 1.91003e+05 -8.73567e+03 -1.66678e+06 1.20730e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39748e+06 2.68001e+05 -1.12947e+06 -1.13183e+06 3.10003e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.79282e+02 6.29797e+01 3.39896e-06 Energy conservation over simulation part #1 of length 31.04 ps, time 0 to 31.04 ps Conserved energy drift: 1.64e-04 kJ/mol/ps per atom <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 15521 steps using 156 frames Energies (kJ/mol) Bond U-B Proper Dih. Per. Imp. Dih. LJ-14 3.94738e+03 1.07162e+04 1.61904e+04 6.09309e+02 4.64438e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 3.87371e+04 1.91022e+05 -8.71092e+03 -1.66858e+06 1.23564e+04 Potential Kinetic En. Total Energy Conserved En. Temperature -1.39906e+06 2.68019e+05 -1.13105e+06 -1.13228e+06 3.10024e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.77703e+02 -8.23883e-01 0.00000e+00 Box-X Box-Y Box-Z 1.01373e+01 1.01373e+01 1.01373e+01 Total Virial (kJ/mol) 8.97077e+04 -7.78832e+01 -2.35026e+02 -7.78179e+01 8.90892e+04 -2.58738e+02 -2.33139e+02 -2.58665e+02 8.93079e+04 Pressure (bar) -1.11397e+01 -4.21625e-01 5.90685e+00 -4.23675e-01 5.79784e+00 5.42839e+00 5.84672e+00 5.42605e+00 2.87017e+00 T-SOLU T-SOLV 3.10016e+02 3.10025e+02 P P - P M E L O A D B A L A N C I N G PP/PME load balancing changed the cut-off and PME settings: particle-particle PME rcoulomb rlist grid spacing 1/beta initial 0.900 nm 0.903 nm 96 96 96 0.105 nm 0.288 nm final 0.949 nm 0.952 nm 80 80 80 0.127 nm 0.304 nm cost-ratio 1.17 0.58 (note that these numbers concern only part of the total PP and PME load) 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 1807.623440 16268.611 0.0 NxN QSTab Elec. + LJ [F] 1290165.658624 52896792.004 97.9 NxN QSTab Elec. + LJ [V&F] 13177.705984 777484.653 1.4 1,4 nonbonded interactions 199.522455 17957.021 0.0 Shift-X 20.020455 120.123 0.0 Bonds 38.678332 2282.022 0.0 Propers 247.420261 56659.240 0.1 Impropers 15.195059 3160.572 0.0 Virial 16.126098 290.270 0.0 Stop-CM 16.016364 160.164 0.0 Calc-Ekin 127.617567 3445.674 0.0 Lincs 37.638425 2258.305 0.0 Lincs-Mat 199.475892 797.904 0.0 Constraint-V 1590.483433 14314.351 0.0 Constraint-Vir 15.707536 376.981 0.0 Settle 505.068861 186875.479 0.3 Urey-Bradley 138.028253 25259.170 0.0 ----------------------------------------------------------------------------- Total 54004502.542 100.0 ----------------------------------------------------------------------------- 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 12 OpenMP threads Activity: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % -------------------------------------------------------------------------------- Neighbor search 1 12 195 1.092 48.393 1.4 Launch PP GPU ops. 1 12 15521 0.784 34.735 1.0 Force 1 12 15521 2.241 99.289 2.9 PME GPU mesh 1 12 15521 31.217 1383.398 40.8 NB X/F buffer ops. 1 12 30847 6.506 288.327 8.5 Write traj. 1 12 2 0.260 11.543 0.3 Update 1 12 15521 3.132 138.791 4.1 Constraints 1 12 15521 2.396 106.167 3.1 Rest 28.894 1280.467 37.8 -------------------------------------------------------------------------------- Total 76.522 3391.111 100.0 -------------------------------------------------------------------------------- Breakdown of PME mesh activities -------------------------------------------------------------------------------- Wait PME GPU gather 1 12 15521 27.819 1232.812 36.4 Reduce GPU PME F 1 12 15521 2.837 125.702 3.7 Launch PME GPU ops. 1 12 139689 0.467 20.717 0.6 -------------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 918.154 76.522 1199.9 (ns/day) (hour/ns) Performance: 35.049 0.685 Finished mdrun on rank 0 Sat May 20 13:37:28 2023