On Thu, 2009-02-12 at 09:28 -0500, Justin A. Lemkul wrote: > > Christian Seifert wrote: > > Hi David, > > > > after reading the man page of g_traj and some tests on its output, I can > > not discover a way of getting the total mass of an index group (e.g. > > protein). > > > > The total mass of the protein is printed by pdb2gmx. Otherwise you can > process > your topology using a Perl script (or something similar) to tally up the > entries > in the mass column.
pdb2gmx is a good hint! The solution to my problem is: 1. make_ndx: grp1 | grp2 | grp3 .. -> grpX 2. pdb2gmx of grpX 3. read the mass for the output Thanks for your help! > > -Justin > > > Cheers, > > Christian. > > > > On Thu, 2009-02-12 at 14:35 +0100, David van der Spoel wrote: > >> Christian Seifert wrote: > >>> Hi users! > >>> > >>> Is there a gmx tool, which calculates the mass of one or more index > >>> groups? The manual says something about a tool named "g_com", but it > >>> seems, as if it does not belong to gmx4.0.3 anymore. > >> try g_traj > >> > >>> Greetings, > >>> Christian. > >>> > >> > -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [email protected] Web: http://www.bph.rub.de _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
