VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon May 07 2012 - 12:55:52 CDT

On Mon, May 7, 2012 at 1:00 PM, patrick wintrode <pat_wde2_at_yahoo.com> wrote:
>
> I've been using VMD to analyze the output of some Gromacs simulations and
> I've found that when I read in a .gro file and then load a .trr trajectory,
> the loading is *extremely* slow compared to .psf .dcd files.
>
> Is there some way to improve this or does VMD just not play well with .trr
> files?

a lot of effort has been spent on optimizing the dcd plugin code,
while next to none went into improving .trr file support.

are you skipping frames when reading files?
this is where the differences would be the largest.

i suspect the first step to get improved support for gromacs
files would be to replace the current code with an interface
to the gromacs fileio library and *then* trying to check for
optimization potential.

axel.

>
> Thanks.
>
> Patrick L. Wintrode
> Department of Pharmaceutical Sciences
> University of Maryland 

--
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.