[gmx-users] mass of a index group
cseifert at bph.ruhr-uni-bochum.de
Thu Feb 12 16:10:52 CET 2009
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!
> > 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
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: cseifert at bph.rub.de
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