NNODES=4, MYRANK=0, HOSTNAME=pople4700.psc.teragrid.org NODEID=0 argc=8 :-) G R O M A C S (-: NNODES=4, MYRANK=1, HOSTNAME=pople4700.psc.teragrid.org NODEID=1 argc=8 NNODES=4, MYRANK=2, HOSTNAME=pople4700.psc.teragrid.org NODEID=2 argc=8 NNODES=4, MYRANK=3, HOSTNAME=pople4700.psc.teragrid.org NODEID=3 argc=8 Good gRace! Old Maple Actually Chews Slate :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, 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. :-) mdrun (-: Option Filename Type Description ------------------------------------------------------------ -s cpeptide_md.tpr Input Generic run input: tpr tpb tpa xml -o cpeptide_md.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c cpeptide_after_md.gro Output Generic structure: gro g96 pdb xml -e ener.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 1 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 yes 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 md0.log to ./#md0.log.2# Back Off! I just backed up md1.log to ./#md1.log.2# Getting Loaded... Reading file cpeptide_md.tpr, VERSION 3.3.3 (single precision) Back Off! I just backed up md2.log to ./#md2.log.2# Back Off! I just backed up md3.log to ./#md3.log.2# Loaded with Money Back Off! I just backed up ener.edr to ./#ener.edr.2# starting mdrun 'Protein in water' 5000 steps, 10.0 ps. Back Off! 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coordinates. step 5000, remaining runtime: 0 s 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 29.565139 975.649587 -0.0 Coulomb 1300.890317 35124.038559 -0.6 Coulomb + LJ 190.789189 7249.989182 -0.1 Outer nonbonded loop -582862.727915 -5828627.279150 100.8 1,4 nonbonded interactions 1.125225 101.270250 -0.0 NS-Pairs 50.221368 1054.648728 -0.0 Reset In Box 0.803604 7.232436 -0.0 Shift-X 16.043208 96.259248 -0.0 CG-CoM 0.272544 7.903776 -0.0 Sum Forces 24.064812 24.064812 -0.0 Angles 1.045209 170.369067 -0.0 Propers 0.370074 84.746946 -0.0 Impropers 0.330066 68.653728 -0.0 Virial 8.921784 160.592112 -0.0 Update 8.021604 248.669724 -0.0 Stop-CM 8.020000 80.200000 -0.0 Calc-Ekin 8.023208 216.626616 -0.0 Lincs 0.720432 43.225920 -0.0 Lincs-Mat 12.547524 50.190096 -0.0 Constraint-V 8.021604 48.129624 -0.0 Constraint-Vir 8.029815 192.715560 -0.0 Settle 2.436461 786.976903 -0.0 ----------------------------------------------------------------------- Total -5781835.126276 100.0 ----------------------------------------------------------------------- NODE (s) Real (s) (%) Time: 9.000 9.000 100.0 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 169.027 -642426.125 96.000 0.250 gcq#49: "I Am Testing Your Grey Matter" (Red Hot Chili Peppers)