Option Filename Type Description ------------------------------------------------------------ -f pr.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c cpeptide_b4pr.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -r cpeptide_b4pr.gro Input, Opt! Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -deshuf deshuf.ndx Output, Opt. Index file -p cpeptide.top Input Topology file -pp processed.top Output, Opt. Topology file -o cpeptide_pr.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene 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 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -np int 4 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# WARNING 1 [file pr.mdp, line unknown]: Unknown left-hand 'warnings' in parameter file checking input for internal consistency... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 2 bonded neighbours for SOL 487 NOTE: System has non-zero total charge: 1.000000e+00 processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K Reading position restraint coords from cpeptide_b4pr.gro renumbering atomtypes... converting bonded parameters... Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Opening library file /usr/local/packages/gromacs/share/gromacs/top/aminoacids.dat WARNING 2 [file aminoacids.dat, line 1]: T-Coupling group protein has fewer than 10% of the atoms (143 out of 1604) Maybe you want to try Protein and Non-Protein instead? Making dummy/rest group for Acceleration containing 1604 elements Making dummy/rest group for Freeze containing 1604 elements Making dummy/rest group for Energy Mon. containing 1604 elements Making dummy/rest group for VCM containing 1604 elements Number of degrees of freedom in T-Coupling group Protein is 284.73 Number of degrees of freedom in T-Coupling group SOL is 2919.27 Making dummy/rest group for User1 containing 1604 elements Making dummy/rest group for User2 containing 1604 elements Making dummy/rest group for XTC containing 1604 elements Making dummy/rest group for Or. Res. Fit containing 1604 elements Making dummy/rest group for QMMM containing 1604 elements T-Coupling has 2 element(s): Protein SOL Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... splitting topology... Walking down the molecule graph to make shake-blocks There are 544 charge group borders and 488 shake borders There are 488 total borders Division over nodes in atoms: 401 402 402 399 writing run input file... There were 2 warnings gcq#205: "Don't Eat That Yellow Snow" (F. Zappa) :-) G R O M A C S (-: Green Red Orange Magenta Azure Cyan Skyblue :-) 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. :-) grompp (-: creating statusfile for 4 nodes... calling /lib/cpp... processing topology... turning all bonds into constraints... turning all bonds into constraints... # G96ANGLES: 209 # PDIHS: 74 # IDIHS: 66 # LJ14: 225 # POSRES: 108 # CONSTR: 144 # SETTLE: 487 Analysing residue names: There are: 487 OTHER residues There are: 13 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other...