NNODES=16, MYRANK=0, HOSTNAME=noco013.nec NNODES=16, MYRANK=1, HOSTNAME=noco013.nec NNODES=16, MYRANK=2, HOSTNAME=noco042.nec NNODES=16, MYRANK=3, HOSTNAME=noco042.nec NNODES=16, MYRANK=5, HOSTNAME=noco066.nec NNODES=16, MYRANK=4, HOSTNAME=noco066.nec NNODES=16, MYRANK=6, HOSTNAME=noco067.nec NNODES=16, MYRANK=7, HOSTNAME=noco067.nec NNODES=16, MYRANK=8, HOSTNAME=noco068.nec NNODES=16, MYRANK=9, HOSTNAME=noco068.nec NNODES=16, MYRANK=11, HOSTNAME=noco072.nec NNODES=16, MYRANK=10, HOSTNAME=noco072.nec NNODES=16, MYRANK=13, HOSTNAME=noco073.nec NNODES=16, MYRANK=12, HOSTNAME=noco073.nec NNODES=16, MYRANK=15, HOSTNAME=noco109.nec NNODES=16, MYRANK=14, HOSTNAME=noco109.nec NODEID=1 argc=11 NODEID=2 argc=11 NODEID=3 argc=11 NODEID=11 argc=11 NODEID=0 argc=11 :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /cacau/rus/itt/ms/bin/mdrun (-: Option Filename Type Description ------------------------------------------------------------ -s ethane_64000.tpr Input Generic run input: tpr tpb tpa xml -o ethane_64000.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c ethane_64000.gro Output Generic structure: gro g96 pdb xml -e ethane_64000.edr Output Generic energy: edr ene -g md.log Output Log file -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file -field field.xvg Output, Opt. xvgr/xmgr file -table table.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.xvg Output, Opt. xvgr/xmgr file -ei sam.edi Input, Opt. ED sampling input -eo sam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jo bam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 19 Set the nicelevel -deffnm string Set the default filename for all file options -[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -np int 16 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -replex int 0 Attempt replica exchange every # steps -reseed int -1 Seed for replica exchange, -1 is generate a seed -[no]glas bool no Do glass simulation with special long range corrections -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system NODEID=5 argc=11 NODEID=6 argc=11 NODEID=4 argc=11 NODEID=7 argc=11 NODEID=8 argc=11 NODEID=9 argc=11 NODEID=13 argc=11 NODEID=10 argc=11 NODEID=12 argc=11 NODEID=15 argc=11 NODEID=14 argc=11 Reading file ethane_64000.tpr, VERSION 3.3.1 (single precision) starting mdrun 'pure ethane' 30000 steps, 99.9 ps. Writing final coordinates. M E G A - F L O P S A C C O U N T I N G Parallel run - timing based on wallclock. RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % of Flops ----------------------------------------------------------------------- LJ 24380.617267 804560.369811 27.4 Outer nonbonded loop 3610.504558 36105.045580 1.2 NS-Pairs 66575.323756 1398081.798876 47.6 Reset In Box 3840.128000 34561.152000 1.2 Shift-X 7680.256000 46081.536000 1.6 CG-CoM 3840.128000 111363.712000 3.8 Sum Forces 30721.024000 30721.024000 1.0 Virial 3853.088432 69355.591776 2.4 Update 3840.128000 119043.968000 4.1 Calc-Ekin 3840.256000 103686.912000 3.5 Lincs 1920.192000 115211.520000 3.9 Constraint-V 3840.128000 23040.768000 0.8 Constraint-Vir 1920.192000 46084.608000 1.6 ----------------------------------------------------------------------- Total 2937898.006043 100.0 ----------------------------------------------------------------------- NODE (s) Real (s) (%) Time: 3124.000 3124.000 100.0 52:04 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 7.804 940.428 2.763 8.686 gcq#2: Thanx for Using GROMACS - Have a Nice Day Cleaning up all processes ... done.