:-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.6.5 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. 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 Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) grompp_mpi (-: Option Filename Type Description ------------------------------------------------------------ -f dynamic.mdp Input grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c equilibration.gro Input Structure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt! Index file -p system.top Input Topology file -pp processed.top Output, Opt. Topology file -o dynamic.tpr Output Run input file: tpr tpb tpa -t equilibration.trr Input, Opt! Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file -ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -[no]v bool no Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 10 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[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 ------------------------------------------------------- Program grompp_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/gmxlib/statutil.c, line: 977 Invalid command line argument: grompp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "You Don't Wanna Know" (Pulp Fiction)