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518 lines
22 KiB
518 lines
22 KiB
:-) GROMACS - gmx mdrun, 2020.6-Debian-2020.6-2 (-: |
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GROMACS is written by: |
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Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen |
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Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd |
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Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray |
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Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang |
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Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis |
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Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson |
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Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund |
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Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall |
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Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov |
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Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen |
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Christian Wennberg Maarten Wolf Artem Zhmurov |
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and the project leaders: |
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Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel |
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Copyright (c) 1991-2000, University of Groningen, The Netherlands. |
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Copyright (c) 2001-2019, The GROMACS development team at |
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Uppsala University, Stockholm University and |
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the Royal Institute of Technology, Sweden. |
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check out http://www.gromacs.org for more information. |
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GROMACS is free software; you can redistribute it and/or modify it |
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under the terms of the GNU Lesser General Public License |
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as published by the Free Software Foundation; either version 2.1 |
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of the License, or (at your option) any later version. |
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GROMACS: gmx mdrun, version 2020.6-Debian-2020.6-2 |
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Executable: /usr/bin/gmx |
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Data prefix: /usr |
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Working dir: /home/student/adit/CMMDE_launching/larutan/SistemLarutan |
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Process ID: 2570742 |
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Command line: |
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gmx -quiet mdrun -deffnm npt -ntmpi 1 -v true |
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GROMACS version: 2020.6-Debian-2020.6-2 |
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Precision: single |
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Memory model: 64 bit |
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MPI library: thread_mpi |
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OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) |
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GPU support: disabled |
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SIMD instructions: SSE4.1 |
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FFT library: fftw-3.3.8-sse2-avx |
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RDTSCP usage: disabled |
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TNG support: enabled |
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Hwloc support: hwloc-2.4.1 |
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Tracing support: disabled |
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C compiler: /usr/bin/cc GNU 10.2.1 |
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C compiler flags: -msse4.1 -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG |
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C++ compiler: /usr/bin/c++ GNU 10.2.1 |
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C++ compiler flags: -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG |
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Running on 1 node with total 1 cores, 2 logical cores |
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Hardware detected: |
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CPU info: |
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Vendor: Intel |
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Brand: Intel(R) Xeon(R) CPU @ 2.20GHz |
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Family: 6 Model: 79 Stepping: 0 |
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Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 x2apic |
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Hardware topology: Full, with devices |
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Sockets, cores, and logical processors: |
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Socket 0: [ 0 1] |
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Numa nodes: |
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Node 0 (8343068672 bytes mem): 0 1 |
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Latency: |
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0 |
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0 1.00 |
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Caches: |
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L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways |
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L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 2 ways |
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L3: 57671680 bytes, linesize 64 bytes, assoc. 20, shared 2 ways |
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PCI devices: |
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0000:00:04.0 Id: 1af4:1000 Class: 0x0200 Numa: 0 |
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Highest SIMD level requested by all nodes in run: AVX2_256 |
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SIMD instructions selected at compile time: SSE4.1 |
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This program was compiled for different hardware than you are running on, |
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which could influence performance. |
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The current CPU can measure timings more accurately than the code in |
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gmx mdrun was configured to use. This might affect your simulation |
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speed as accurate timings are needed for load-balancing. |
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Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. |
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|
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. |
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Lindahl |
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GROMACS: High performance molecular simulations through multi-level |
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parallelism from laptops to supercomputers |
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SoftwareX 1 (2015) pp. 19-25 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl |
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with |
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GROMACS |
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. |
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl |
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GROMACS 4.5: a high-throughput and highly parallel open source molecular |
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simulation toolkit |
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Bioinformatics 29 (2013) pp. 845-54 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl |
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable |
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molecular simulation |
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J. Chem. Theory Comput. 4 (2008) pp. 435-447 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. |
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Berendsen |
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GROMACS: Fast, Flexible and Free |
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J. Comp. Chem. 26 (2005) pp. 1701-1719 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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E. Lindahl and B. Hess and D. van der Spoel |
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GROMACS 3.0: A package for molecular simulation and trajectory analysis |
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J. Mol. Mod. 7 (2001) pp. 306-317 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen |
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GROMACS: A message-passing parallel molecular dynamics implementation |
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Comp. Phys. Comm. 91 (1995) pp. 43-56 |
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-------- -------- --- Thank You --- -------- -------- |
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The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1 |
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Input Parameters: |
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integrator = md |
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tinit = 0 |
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dt = 0.002 |
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nsteps = 1000 |
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init-step = 0 |
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simulation-part = 1 |
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comm-mode = Linear |
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nstcomm = 100 |
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bd-fric = 0 |
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ld-seed = 1509818253 |
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emtol = 10 |
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emstep = 0.01 |
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niter = 20 |
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fcstep = 0 |
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nstcgsteep = 1000 |
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nbfgscorr = 10 |
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rtpi = 0.05 |
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nstxout = 500 |
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nstvout = 500 |
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nstfout = 0 |
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nstlog = 500 |
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nstcalcenergy = 100 |
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nstenergy = 500 |
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nstxout-compressed = 0 |
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compressed-x-precision = 1000 |
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cutoff-scheme = Verlet |
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nstlist = 10 |
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pbc = xyz |
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periodic-molecules = false |
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verlet-buffer-tolerance = 0.005 |
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rlist = 0.961399 |
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coulombtype = PME |
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coulomb-modifier = Potential-shift |
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rcoulomb-switch = 0 |
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rcoulomb = 0.961399 |
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epsilon-r = 1 |
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epsilon-rf = inf |
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vdw-type = Cut-off |
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vdw-modifier = Potential-shift |
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rvdw-switch = 0 |
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rvdw = 0.961399 |
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DispCorr = EnerPres |
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table-extension = 1 |
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fourierspacing = 0.16 |
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fourier-nx = 14 |
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fourier-ny = 14 |
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fourier-nz = 14 |
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pme-order = 4 |
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ewald-rtol = 1e-05 |
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ewald-rtol-lj = 0.001 |
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lj-pme-comb-rule = Geometric |
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ewald-geometry = 0 |
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epsilon-surface = 0 |
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tcoupl = V-rescale |
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nsttcouple = 10 |
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nh-chain-length = 0 |
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print-nose-hoover-chain-variables = false |
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pcoupl = Berendsen |
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pcoupltype = Isotropic |
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nstpcouple = 10 |
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tau-p = 2 |
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compressibility (3x3): |
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compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} |
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compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} |
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compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} |
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ref-p (3x3): |
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ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} |
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ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} |
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ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} |
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refcoord-scaling = COM |
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posres-com (3): |
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posres-com[0]= 0.00000e+00 |
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posres-com[1]= 0.00000e+00 |
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posres-com[2]= 0.00000e+00 |
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posres-comB (3): |
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posres-comB[0]= 0.00000e+00 |
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posres-comB[1]= 0.00000e+00 |
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posres-comB[2]= 0.00000e+00 |
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QMMM = false |
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QMconstraints = 0 |
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QMMMscheme = 0 |
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MMChargeScaleFactor = 1 |
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qm-opts: |
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ngQM = 0 |
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constraint-algorithm = Lincs |
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continuation = true |
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Shake-SOR = false |
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shake-tol = 0.0001 |
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lincs-order = 4 |
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lincs-iter = 1 |
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lincs-warnangle = 30 |
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nwall = 0 |
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wall-type = 9-3 |
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wall-r-linpot = -1 |
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wall-atomtype[0] = -1 |
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wall-atomtype[1] = -1 |
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wall-density[0] = 0 |
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wall-density[1] = 0 |
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wall-ewald-zfac = 3 |
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pull = false |
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awh = false |
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rotation = false |
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interactiveMD = false |
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disre = No |
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disre-weighting = Conservative |
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disre-mixed = false |
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dr-fc = 1000 |
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dr-tau = 0 |
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nstdisreout = 100 |
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orire-fc = 0 |
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orire-tau = 0 |
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nstorireout = 100 |
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free-energy = no |
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cos-acceleration = 0 |
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deform (3x3): |
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deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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simulated-tempering = false |
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swapcoords = no |
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userint1 = 0 |
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userint2 = 0 |
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userint3 = 0 |
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userint4 = 0 |
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userreal1 = 0 |
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userreal2 = 0 |
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userreal3 = 0 |
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userreal4 = 0 |
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applied-forces: |
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electric-field: |
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x: |
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E0 = 0 |
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omega = 0 |
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t0 = 0 |
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sigma = 0 |
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y: |
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E0 = 0 |
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omega = 0 |
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t0 = 0 |
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sigma = 0 |
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z: |
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E0 = 0 |
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omega = 0 |
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t0 = 0 |
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sigma = 0 |
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density-guided-simulation: |
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active = false |
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group = protein |
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similarity-measure = inner-product |
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atom-spreading-weight = unity |
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force-constant = 1e+09 |
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gaussian-transform-spreading-width = 0.2 |
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gaussian-transform-spreading-range-in-multiples-of-width = 4 |
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reference-density-filename = reference.mrc |
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nst = 1 |
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normalize-densities = true |
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adaptive-force-scaling = false |
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adaptive-force-scaling-time-constant = 4 |
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grpopts: |
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nrdf: 1012 |
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ref-t: 298.15 |
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tau-t: 0.1 |
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annealing: No |
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annealing-npoints: 0 |
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acc: 0 0 0 |
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nfreeze: N N N |
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energygrp-flags[ 0]: 0 |
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Changing nstlist from 10 to 100, rlist from 0.961399 to 0.966399 |
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Using 1 MPI thread |
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Non-default thread affinity set, disabling internal thread affinity |
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Using 1 OpenMP thread |
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System total charge: -0.000 |
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Will do PME sum in reciprocal space for electrostatic interactions. |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen |
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A smooth particle mesh Ewald method |
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J. Chem. Phys. 103 (1995) pp. 8577-8592 |
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-------- -------- --- Thank You --- -------- -------- |
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Using a Gaussian width (1/beta) of 0.307804 nm for Ewald |
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Potential shift: LJ r^-12: -1.604e+00 r^-6: -1.266e+00, Ewald -1.040e-05 |
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Initialized non-bonded Ewald tables, spacing: 9.15e-04 size: 1052 |
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Generated table with 983 data points for 1-4 COUL. |
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Tabscale = 500 points/nm |
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Generated table with 983 data points for 1-4 LJ6. |
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Tabscale = 500 points/nm |
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Generated table with 983 data points for 1-4 LJ12. |
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Tabscale = 500 points/nm |
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Using SIMD 4x4 nonbonded short-range kernels |
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Using a 4x4 pair-list setup: |
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updated every 100 steps, buffer 0.005 nm, rlist 0.966 nm |
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At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: |
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updated every 100 steps, buffer 0.178 nm, rlist 1.139 nm |
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Using Lorentz-Berthelot Lennard-Jones combination rule |
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Long Range LJ corr.: <C6> 3.6868e-04 |
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Initializing LINear Constraint Solver |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije |
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LINCS: A Linear Constraint Solver for molecular simulations |
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J. Comp. Chem. 18 (1997) pp. 1463-1472 |
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-------- -------- --- Thank You --- -------- -------- |
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The number of constraints is 281 |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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G. Bussi, D. Donadio and M. Parrinello |
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Canonical sampling through velocity rescaling |
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J. Chem. Phys. 126 (2007) pp. 014101 |
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-------- -------- --- Thank You --- -------- -------- |
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There are: 432 Atoms |
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Center of mass motion removal mode is Linear |
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We have the following groups for center of mass motion removal: |
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0: rest |
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Started mdrun on rank 0 Tue Jun 7 16:54:19 2022 |
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Step Time |
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0 0.00000 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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3.51747e+01 1.84321e+02 3.77233e+01 7.31505e+01 -4.79605e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.52513e+03 -3.16425e+02 -3.37410e+01 2.95999e+02 7.23590e+01 |
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Potential Kinetic En. Total Energy Conserved En. Temperature |
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-2.18136e+03 1.21869e+03 -9.62671e+02 -9.62789e+02 2.89674e+02 |
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Pres. DC (bar) Pressure (bar) Constr. rmsd |
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-5.87450e+01 6.96512e+02 3.57903e-06 |
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Step Time |
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500 1.00000 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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2.41304e+01 2.09645e+02 3.48747e+01 6.12608e+01 -4.82812e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.52196e+03 -3.09200e+02 -3.33474e+01 2.78813e+02 7.70100e+01 |
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Potential Kinetic En. Total Energy Conserved En. Temperature |
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-2.18360e+03 1.26907e+03 -9.14526e+02 -9.56705e+02 3.01649e+02 |
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Pres. DC (bar) Pressure (bar) Constr. rmsd |
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-5.73865e+01 4.31256e+02 3.11114e-06 |
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Step Time |
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1000 2.00000 |
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Writing checkpoint, step 1000 at Tue Jun 7 16:54:19 2022 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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1.68244e+01 2.08255e+02 3.52075e+01 5.01472e+01 -4.69767e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.50504e+03 -3.10979e+02 -3.31481e+01 3.10664e+02 6.80086e+01 |
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Potential Kinetic En. Total Energy Conserved En. Temperature |
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-2.16475e+03 1.17078e+03 -9.93974e+02 -9.56017e+02 2.78286e+02 |
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Pres. DC (bar) Pressure (bar) Constr. rmsd |
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-5.67048e+01 -1.28313e+02 2.51029e-06 |
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<====== ############### ==> |
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<==== A V E R A G E S ====> |
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<== ############### ======> |
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Statistics over 1001 steps using 11 frames |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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3.24381e+01 1.97069e+02 4.05481e+01 7.07486e+01 -4.78417e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.52312e+03 -3.00815e+02 -3.34046e+01 3.03795e+02 7.23368e+01 |
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Potential Kinetic En. Total Energy Conserved En. Temperature |
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-2.14518e+03 1.23575e+03 -9.09432e+02 -9.58358e+02 2.93729e+02 |
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Pres. DC (bar) Pressure (bar) Constr. rmsd |
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-5.75851e+01 5.91769e+02 0.00000e+00 |
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Box-X Box-Y Box-Z |
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2.12989e+00 2.12989e+00 2.12989e+00 |
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Total Virial (kJ/mol) |
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1.93100e+02 -2.49378e+01 1.84712e+01 |
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-2.49377e+01 2.38996e+02 1.06244e+01 |
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1.84713e+01 1.06244e+01 2.88781e+02 |
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Pressure (bar) |
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8.26414e+02 7.31564e+01 -1.08744e+02 |
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7.31561e+01 4.88213e+02 -2.96331e+01 |
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-1.08744e+02 -2.96331e+01 4.60678e+02 |
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M E G A - F L O P S A C C O U N T I N G |
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NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels |
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RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table |
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W3=SPC/TIP3p W4=TIP4p (single or pairs) |
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V&F=Potential and force V=Potential only F=Force only |
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Computing: M-Number M-Flops % Flops |
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----------------------------------------------------------------------------- |
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Pair Search distance check 0.789264 7.103 0.2 |
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NxN QSTab Elec. + LJ [F] 53.170128 2179.975 53.2 |
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NxN QSTab Elec. + LJ [V&F] 0.590864 34.861 0.9 |
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NxN QSTab Elec. [F] 28.800288 979.210 23.9 |
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NxN QSTab Elec. [V&F] 0.321440 13.179 0.3 |
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1,4 nonbonded interactions 0.072072 6.486 0.2 |
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Calc Weights 1.297296 46.703 1.1 |
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Spread Q Bspline 27.675648 55.351 1.3 |
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Gather F Bspline 27.675648 166.054 4.0 |
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3D-FFT 62.746684 501.973 12.2 |
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Solve PME 0.196196 12.557 0.3 |
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Shift-X 0.004752 0.029 0.0 |
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Bonds 0.027027 1.595 0.0 |
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Angles 0.226226 38.006 0.9 |
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Propers 0.027027 6.189 0.2 |
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RB-Dihedrals 0.072072 17.802 0.4 |
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Virial 0.048177 0.867 0.0 |
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Stop-CM 0.004752 0.048 0.0 |
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P-Coupling 0.043632 0.262 0.0 |
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Calc-Ekin 0.087264 2.356 0.1 |
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Lincs 0.281281 16.877 0.4 |
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Lincs-Mat 1.957956 7.832 0.2 |
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Constraint-V 0.562562 4.500 0.1 |
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Constraint-Vir 0.028381 0.681 0.0 |
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----------------------------------------------------------------------------- |
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Total 4100.496 100.0 |
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----------------------------------------------------------------------------- |
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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 |
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On 1 MPI rank |
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Computing: Num Num Call Wall time Giga-Cycles |
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Ranks Threads Count (s) total sum % |
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----------------------------------------------------------------------------- |
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Neighbor search 1 1 11 0.009 0.020 1.4 |
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Force 1 1 1001 0.425 0.935 66.2 |
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PME mesh 1 1 1001 0.143 0.315 22.3 |
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NB X/F buffer ops. 1 1 1991 0.005 0.012 0.8 |
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Write traj. 1 1 3 0.023 0.050 3.5 |
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Update 1 1 1001 0.005 0.010 0.7 |
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Constraints 1 1 1001 0.023 0.051 3.6 |
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Rest 0.009 0.019 1.4 |
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----------------------------------------------------------------------------- |
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Total 0.642 1.413 100.0 |
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----------------------------------------------------------------------------- |
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Breakdown of PME mesh computation |
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----------------------------------------------------------------------------- |
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PME spread 1 1 1001 0.041 0.090 6.4 |
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PME gather 1 1 1001 0.057 0.126 8.9 |
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PME 3D-FFT 1 1 2002 0.026 0.056 4.0 |
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PME solve Elec 1 1 1001 0.018 0.040 2.8 |
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----------------------------------------------------------------------------- |
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Core t (s) Wall t (s) (%) |
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Time: 0.642 0.642 100.0 |
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(ns/day) (hour/ns) |
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Performance: 269.397 0.089 |
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Finished mdrun on rank 0 Tue Jun 7 16:54:19 2022 |
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