VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Feb 21 2008 - 06:58:52 CST

On Thu, 21 Feb 2008, maria goranovic wrote:

MG> Hi VMDers
MG>

maria,

MG> VMD can read gromacs trajectories. Can it do standard analysis on
MG> them ? If so, how does one read them from the command line ?

VMD does not care where information is coming from, so as long
as there is a reader plugin, it can use the information for
visualization and analysis. VMD can read .xtc, .trr, .gro, .pdb,
.g96 files but not .tpr or .top files. there was a converter for
preprocessed topologies to .psf(?) somewhere in the script library.

i don't know, what you understand as "standard analysis" (everybody
will define this differently). reading from the command line works
like with other file types. without a flag VMD tries to guess the
fromat from the filename other than that you can provide the
file type with a flag, .e.g -trr for .trr files -pdb for .pdb and
so on. this is all explained in detail in the VMD user's guide.
i suggest you have a look at that and at the VMD plugin documentation
(both available on-line on the VMD home page) to see if VMD fits
your bill.

cheers,
   axel.

MG>
MG> Thank u
MG>
MG> -maria
MG>
MG> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.