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Hi,<br><br>You have an error in your input file.<br>Does grompp also hang with correct mdp parameters?<br><br>Berk<br><br>> Date: Thu, 21 May 2009 23:55:32 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] grompp 4.0.5 hangs while 3.2.1 works<br>> <br>> Kaihsu Tai wrote:<br>> > I have a system which works with grompp 3.2.1 but grompp <br>> > 4.0.5 hangs at ‘processing topology...’. Is there something <br>> > that had changed (say, file format in .top or .itp) that <br>> > could have caused this? I can supply my topology, <br>> > conformation, etc. files if necessary for debugging. Cheers.<br>> > <br>> > $ grompp -v -f test0_.mdp -po test0.mdp -c initial.gro -p Kir21.top -o test0.tpr<br>> > :-) G R O M A C S (-:<br>> > <br>> > GROwing Monsters And Cloning Shrimps<br>> > <br>> > :-) VERSION 4.0.5 (-:<br>> > <br>> > <br>> > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>> > Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>> > Copyright (c) 2001-2008, The GROMACS development team,<br>> > check out http://www.gromacs.org for more information.<br>> > <br>> > This program is free software; you can redistribute it and/or<br>> > modify it under the terms of the GNU General Public License<br>> > as published by the Free Software Foundation; either version 2<br>> > of the License, or (at your option) any later version.<br>> > <br>> > :-) grompp (-:<br>> > <br>> > Option Filename Type Description<br>> > ------------------------------------------------------------<br>> > -f test0_.mdp Input, Opt! grompp input file with MD parameters<br>> > -po test0.mdp Output grompp input file with MD parameters<br>> > -c initial.gro Input Structure file: gro g96 pdb tpr tpb tpa<br>> > -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>> > -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>> > -n index.ndx Input, Opt. Index file<br>> > -p Kir21.top Input Topology file<br>> > -pp processed.top Output, Opt. Topology file<br>> > -o test0.tpr Output Run input file: tpr tpb tpa<br>> > -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br>> > -e ener.edr Input, Opt. Energy file: edr ene<br>> > <br>> > Option Type Value Description<br>> > ------------------------------------------------------<br>> > -[no]h bool no Print help info and quit<br>> > -nice int 0 Set the nicelevel<br>> > -[no]v bool yes Be loud and noisy<br>> > -time real -1 Take frame at or first after this time.<br>> > -[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br>> > sites<br>> > -maxwarn int 0 Number of allowed warnings during input processing<br>> > -[no]zero bool no Set parameters for bonded interactions without<br>> > defaults to zero instead of generating an error<br>> > -[no]renum bool yes Renumber atomtypes and minimize number of<br>> > atomtypes<br>> > <br>> > Ignoring obsolete mdp entry 'title'<br>> > Ignoring obsolete mdp entry 'cpp'<br>> > <br>> > Back Off! I just backed up test0.mdp to ./#test0.mdp.7#<br>> > checking input for internal consistency...<br>> > <br>> > NOTE 1 [file test0_.mdp, line unknown]:<br>> > The Berendsen thermostat does not generate the correct kinetic energy<br>> > distribution. You might want to consider using the V-rescale thermostat.<br>> > <br>> > <br>> > ERROR: With coulombtype = PME, rcoulomb must be equal to rlist<br>> > If you want optimal energy conservation or exact integration use PME-Switch<br>> > <br>> > processing topology...<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> Please submit a bugzilla with all input files to reproduce the problem.<br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone:        +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se        spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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