On 10/6/16 8:23 AM, Menig, Simon wrote:
Thank you for your fast answer Justin
I looked up the log files but I found no error and my disc space is sufficient
and the simulation seem to end normal. Could the Problem be that my Simulation
time is shorter than 15 min (max 5000 steps) ? (Shouldn't it write a cpt file
after the End of the simulation)
Parts of my log file:
Log file opened on Thu Oct 6 14:09:27 2016
Host: linux-286u pid: 4384 rank ID: 0 number of ranks: 1
:-) GROMACS - gmx mdrun, 2016 (-:
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:
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check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
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GROMACS: gmx mdrun, version 2016
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/simon/simu_test_cg/build_cg_membrane_test1
Command line:
gmx mdrun -s input/ab26_wt_POPE_POPG_cg_eqi_1.tpr -o
out_trr/ab26_wt_POPE_POPG_cg_eqi_1.trr -c output/ab26_wt_POPE_POPG_cg_eqi_1.gro
-e output/ab26_wt_POPE_POPG_cg_eqi_1.edr -g
output/ab26_wt_POPE_POPG_cg_eqi_1.log -cpo output/ab26_wt_POPE_POPG_cg_eqi_1 -v
-cpt 1
GROMACS version: 2016
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support: disabled
SIMD instructions: AVX_256
FFT library: fftw-3.3.4-sse2-avx
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
Built on: Do 1. Sep 09:46:51 CEST 2016
Built by: simon@linux-286u [CMAKE]
Build OS/arch: Linux 4.1.12-1-default x86_64
Build CPU vendor: Intel
Build CPU brand: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz
Build CPU family: 6 Model: 45 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf mmx msr
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 4.8.5
C compiler flags: -mavx -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
C++ compiler: /usr/bin/c++ GNU 4.8.5
C++ compiler flags: -mavx -std=c++0x -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
Running on 1 node with total 4 cores, 8 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz
Family: 6 Model: 45 Stepping: 7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf mmx msr nonstop_tsc
pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt
x2apic
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256
Hardware topology: Basic
Sockets, cores, and logical processors:
Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7]
-----------------------------------------
Energies (kJ/mol)
Bond G96Angle Proper Dih. LJ (SR) Coulomb (SR)
1.36475e+04 2.16816e+04 1.59230e+03 -2.94378e+06 -2.60982e+04
Potential Pressure (bar) Constr. rmsd
-2.93295e+06 -8.86450e+01 5.54635e-06
Steepest Descents converged to Fmax < 100 in 3325 steps
Potential Energy = -2.9329548e+06
Maximum force = 9.9675224e+01 on atom 3030
Norm of force = 3.0542336e+00
You're doing energy minimization. There is no checkpointing in EM.
As an aside, you also did not provide accurate information in your previous
message. You said you were using 5.1 but your .log indicates you are using
2016, and your command line was different. While it didn't matter here, please
*always* provide accurate information to reach a resolution as quickly as
possible. Had there been some problem, we would have tried to reproduce it with
5.1, which would have been entirely unproductive.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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