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- | | | | | :-) GROMACS - gmx mdrun, 2016.4 (-:
- | | | | | | GROMACS is written by:
- |Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
- Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
- Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
- Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
- Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
- Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
- Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
- Teemu Virolainen Christian Wennberg Maarten Wolf
- | | | | | | 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) 2001-2017, The GROMACS development team at
- Uppsala University, Stockholm University and
- the Royal Institute of Technology, Sweden.
- check out http://www.gromacs.org for more information.
- GROMACS is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License
- as published by the Free Software Foundation; either version 2.1
- of the License, or (at your option) any later version.
- GROMACS: gmx mdrun, version 2016.4
- Executable: /home/hoemberg/SOFTWARE/GROMACS/GMX_2016.4_AVX2/bin/gmx_mpi
- Data prefix: /home/hoemberg/SOFTWARE/GROMACS/GMX_2016.4_AVX2
- Working dir: /home/hoemberg/ADK/PRESSURE/EADK/CLOSED/TMD_KAPPA_TEST/GPU/TMD_1000_GPU
- Command line:
- gmx_mpi mdrun -pin on -pinoffset 0 -gpu_id 0 -ntomp 8 -v -cpi -s TMD_1000.tpr -o TMD_1000.trr -x TMD_1000.xtc -g TMD_1000.log -c eADK_TMD_1000.gro
- Warning: No checkpoint file found with -cpi option. Assuming this is a new run.
- Running on 1 node with total 16 cores, 16 logical cores, 4 compatible GPUs
- Hardware detected on host gpu-compute-5-8.local (the node of MPI rank 0):
- CPU info:
- Vendor: Intel
- Brand: Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
- SIMD instructions most likely to fit this hardware: AVX_256
- SIMD instructions selected at GROMACS compile time: SSE4.1
- Hardware topology: Basic
- GPU info:
- Number of GPUs detected: 4
- #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible
- #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible
- #2: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible
- #3: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible
- Compiled SIMD instructions: SSE4.1, GROMACS could use AVX_256 on this machine, which is better.
- Reading file TMD_1000.tpr, VERSION 2016.4 (single precision)
- Changing nstlist from 10 to 40, rlist from 1.2 to 1.28
- Using 1 MPI process
- Using 8 OpenMP threads
- 1 GPU user-selected for this run.
- Mapping of GPU ID to the 1 PP rank in this node: 0
- Overriding thread affinity set outside gmx mdrun
- starting mdrun 'eADK in Water'
- 26000000 steps, 52000.0 ps.
- ^Mstep 80: timed with pme grid 72 72 72, coulomb cutoff 1.200: 563.4 M-cycles
- ^Mstep 160: timed with pme grid 60 60 60, coulomb cutoff 1.280: 508.9 M-cycles
- Step 222, time 0.444 (ps) LINCS WARNING
- relative constraint deviation after LINCS:
- rms 0.000020, max 0.000432 (between atoms 2101 and 2102)
- bonds that rotated more than 30 degrees:
- atom 1 atom 2 angle previous, current, constraint length
- 2101 2103 34.0 0.1178 0.1111 0.1111
- Step 223, time 0.446 (ps) LINCS WARNING
- relative constraint deviation after LINCS:
- rms 0.000082, max 0.002613 (between atoms 2101 and 2103)
- bonds that rotated more than 30 degrees:
- atom 1 atom 2 angle previous, current, constraint length
- 2101 2103 35.2 0.1105 0.1114 0.1111
- Step 228, time 0.456 (ps) LINCS WARNING
- relative constraint deviation after LINCS:
- rms 0.005702, max 0.257592 (between atoms 2101 and 2102)
- bonds that rotated more than 30 degrees:
- atom 1 atom 2 angle previous, current, constraint length
- 2101 2102 90.0 0.1111 0.1397 0.1111
- 2104 2106 90.0 0.1111 0.1348 0.1111
- Step 229, time 0.458 (ps) LINCS WARNING
- relative constraint deviation after LINCS:
- rms 0.001372, max 0.080100 (between atoms 2101 and 2102)
- bonds that rotated more than 30 degrees:
- atom 1 atom 2 angle previous, current, constraint length
- 2101 2102 90.0 0.1397 0.1200 0.1111
- 2104 2106 75.4 0.1348 0.1109 0.1111
- Step 230, time 0.46 (ps) LINCS WARNING
- relative constraint deviation after LINCS:
- rms 0.003682, max 0.173647 (between atoms 2101 and 2102)
- bonds that rotated more than 30 degrees:
- atom 1 atom 2 angle previous, current, constraint length
- 2101 2102 90.0 0.1200 0.1304 0.1111
- 2104 2106 90.0 0.1109 0.1254 0.1111
- Step 231, time 0.462 (ps) LINCS WARNING
- relative constraint deviation after LINCS:
- rms 172.973862, max 7198.149414 (between atoms 2104 and 2105)
- bonds that rotated more than 30 degrees:
- atom 1 atom 2 angle previous, current, constraint length
- 2098 2101 55.5 0.1528 0.0888 0.1530
- 2101 2102 132.5 0.1304 796.0084 0.1111
- 2101 2103 90.0 0.1121 3.2097 0.1111
- 2101 2104 90.4 0.1531 0.3915 0.1530
- 2104 2106 89.9 0.1254 0.6856 0.1111
- 2104 2107 90.4 0.1474 0.2691 0.1480
- 2107 2108 90.5 0.1040 0.0861 0.1040
- 2107 2109 90.3 0.1039 0.0785 0.1040
- 2107 2110 90.4 0.1041 0.0993 0.1040
- Wrote pdb files with previous and current coordinates
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