-bash-3.00$ /usr/bin/time mdrun -s topol.tpr :-) G R O M A C S (-: Great Red Oystrich Makes All Chemists Sane :-) 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. :-) mdrun (-: Option Filename Type Description ------------------------------------------------------------ -s topol.tpr Input Generic run input: tpr tpb tpa xml -o traj.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c confout.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 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 Reading file topol.tpr, VERSION 3.3.1 (single precision) starting mdrun 'ICE in water' 100000 steps, 200.0 ps. Writing final coordinates. M E G A - F L O P S A C C O U N T I N G 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 1517.947935 50092.281855 4.0 Coulomb + LJ [W3-W3] 3741.056609 916558.869205 73.9 Outer nonbonded loop 873.365538 8733.655380 0.7 1,4 nonbonded interactions 55.200552 4968.049680 0.4 NS-Pairs 8996.969826 188936.366346 15.2 Reset In Box 51.122556 460.103004 0.0 Shift-X 511.205112 3067.230672 0.2 CG-CoM 18.960948 549.867492 0.0 Bonds 20.400204 877.208772 0.1 Angles 38.400384 6259.262592 0.5 Propers 20.400204 4671.646716 0.4 Virial 258.302583 4649.446494 0.4 Update 255.602556 7923.679236 0.6 Stop-CM 255.600000 2556.000000 0.2 Calc-Ekin 255.605112 6901.338024 0.6 Constraint-V 255.602556 1533.615336 0.1 Constraint-Vir 241.207236 5788.973664 0.5 Settle 80.402412 25969.979076 2.1 ----------------------------------------------------------------------- Total 1240497.573544 100.0 ----------------------------------------------------------------------- NODE (s) Real (s) (%) Time: 759.510 760.000 99.9 12:39 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 6.924 1.633 22.752 1.055 gcq#37: "They Were So Quiet About It" (Pixies) 759.34user 0.20system 12:40.04elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (19major+1202minor)pagefaults 0swaps -bash-3.00$