Hi Saeed, Just before [ molecules ] insert the lines:
[ system ] A box of water Cheers, Tsjerk On Apr 2, 2016 8:06 AM, "Saeed Nasiri" <s.t.nas...@gmail.com> wrote: > Dear users > > I have constructed a box of only water molecules, but I don't know how to > constructed the topology file. I wrote this file but it didn't work. > > Some commentary will be very appreciated. > Thank you for advance. > > ************************************* topol.top * > ************************************************* > ; > #include "oplsaa.ff/forcefield.itp" > ; Include water topology > #include "oplsaa.ff/tip3p.itp" > > > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > [ molecules ] > SOL 1690 > > *********************************************************************************************** > *~/Desktop/water_box $ gmx_mpi grompp -f minim.mdp -c water_box.gro -o > em.tpr -p topol.top * > :-) GROMACS - gmx grompp, VERSION 5.1.2 (-: > > GROMACS is written by: > Emile Apol Rossen Apostolov Herman J.C. Berendsen Par > Bjelkmar > Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch > Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent > Hindriksen > Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten > Kutzner > Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff > Erik Marklund Teemu Murtola Szilard Pall Sander Pronk > Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers > Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf > and the project leaders: > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2015, The GROMACS development team at > Uppsala University, Stockholm University and > the Royal Institute of Technology, Sweden. > check out http://www.gromacs.org for more information. > > GROMACS 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. > > GROMACS: gmx grompp, VERSION 5.1.2 > Executable: /usr/local/gromacs/bin/gmx_mpi > Data prefix: /usr/local/gromacs > Command line: > gmx_mpi grompp -f minim.mdp -c water_box.gro -o em.tpr -p topol.top > > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4# > > NOTE 1 [file minim.mdp]: > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note > that with the Verlet scheme, nstlist has no effect on the accuracy of > your simulation. > > Setting the LD random seed to 2889297176 > Generated 330891 of the 330891 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 330891 of the 330891 1-4 parameter combinations > > ------------------------------------------------------- > Program gmx grompp, VERSION 5.1.2 > Source code file: > /home/nasiri/gromacs-5.1.2/src/gromacs/gmxpreprocess/topio.c, line: 755 > > > > > > *Fatal error:Syntax error - File topol.top, line 15Last line read:'[ > molecules ]'Invalid order for directive molecules* > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > Halting program gmx grompp > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode 1. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -------------------------------------------------------------------------- > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
