NNODES=8, MYRANK=0, HOSTNAME=noco117.nec NNODES=8, MYRANK=1, HOSTNAME=noco117.nec NNODES=8, MYRANK=2, HOSTNAME=noco118.nec NNODES=8, MYRANK=5, HOSTNAME=noco119.nec NNODES=8, MYRANK=3, HOSTNAME=noco118.nec NNODES=8, MYRANK=4, HOSTNAME=noco119.nec NNODES=8, MYRANK=7, HOSTNAME=noco120.nec NNODES=8, MYRANK=6, HOSTNAME=noco120.nec NODEID=0 argc=11 :-) G R O M A C S (-: NODEID=1 argc=11 NODEID=2 argc=11 NODEID=7 argc=11 NODEID=5 argc=11 NODEID=4 argc=11 NODEID=6 argc=11 NODEID=3 argc=11 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_32768.tpr Input Generic run input: tpr tpb tpa xml -o ethane_32768.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c ethane_32768.gro Output Generic structure: gro g96 pdb xml -e ethane_32768.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 8 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 Back Off! I just backed up md3.log to ./#md3.log.1# Back Off! I just backed up md1.log to ./#md1.log.2# Back Off! I just backed up md2.log to ./#md2.log.1# Back Off! I just backed up md0.log to ./#md0.log.2# Reading file ethane_32768.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 13121.971521 433025.060193 28.3 Outer nonbonded loop 1906.495129 19064.951290 1.2 NS-Pairs 34721.874846 729159.371766 47.6 Reset In Box 1966.145536 17695.309824 1.2 Shift-X 3932.291072 23593.746432 1.5 CG-CoM 1966.145536 57018.220544 3.7 Sum Forces 7864.582144 7864.582144 0.5 Virial 1972.625752 35507.263536 2.3 Update 1966.145536 60950.511616 4.0 Calc-Ekin 1966.211072 53087.698944 3.5 Lincs 983.138304 58988.298240 3.9 Constraint-V 1966.145536 11796.873216 0.8 Constraint-Vir 983.138304 23595.319296 1.5 ----------------------------------------------------------------------- Total 1531347.207041 100.0 ----------------------------------------------------------------------- NODE (s) Real (s) (%) Time: 1946.000 1946.000 100.0 32:26 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 6.743 786.920 4.435 5.411 gcq#2: Thanx for Using GROMACS - Have a Nice Day Cleaning up all processes ... done.