VMD-L Mailing List

From: Glenn Johnson (gjohnson_at_srrc.ars.usda.gov)
Date: Mon Mar 21 2005 - 10:39:00 CST

On Wed, 2005-02-23 at 21:29 +0100, Axel Kohlmeyer wrote:

> hi,
>
> just one remark: the gromacs plugin of the latest VMD (1.8.3)
> should be able to write proper .trr trajectory files
> (exactly to be able to use the gromacs tools for analysis).
> you may prefer those over .pdb trajectories as they are binary
> and thus are read _much_ faster.
>
> axel.

I have converted a .dcd file from NAMD to a Gromacs .trr file. When I
try to use, for example, g_covar, the command fails because it needs
a .tpr file. According to the help blurb for g_covar, that file is a
"Structure+mass(db)" file but can be in .pdb format. Is there a way to
generate this file? If I need to edit it manually, in what column of
the .pdb file would I place the mass values?

Thanks.

>>> "JG" == Justin Gullingsrud <justinrocks_at_gmail.com> writes:

> JG> I've used the Gromacs programs g_covar and g_anaeig to perform
> JG> analysis of NAMD-generated trajectory files by first converting the
> JG> trajectory to sequential pdb format. You can do this in VMD by simply
> JG> loading the dcd file and saving it as a pdb, but there is one caveat:
> JG> you must change all the "END" lines to "ENDMDL", or g_covar will
> JG> crash.
>
> JG> Hope this helps,
> JG> Justin 

-- 
Glenn Johnson <gjohnson_at_srrc.ars.usda.gov>
U. S. Department of Agriculture