VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 10 2011 - 09:51:58 CST

Francesco,
  Thanks for pointing this out. We weren't previously aware
of this patch. It is already too late to make this kind of change
for the VMD 1.9 release, but I agree that adding this functionality
to psfgen is a good idea. The one thing about this patch is that
it adds more code that does things "the old way". We have been
slowly rewriting psfgen so that it uses the VMD plugins to
read and write files rather than having hard-coded file reading
and writing code. We've been testing this functionality internally
in our lab for some time now (e.g. this is currently the only way to use
psfgen to build huge 100M atom structures), but it isn't enabled in the
default builds included with VMD just yet. What I would like to see happen
(if it is feasible) is for this Gromacs patch for psfgen to be reorganized
so that it works through the new plugin-based mechanisms in psfgen.
In principle that should make it simpler, and another benefit will
be that VMD and psfgen would both end up being able to read and write
the Gromacs topology files. I haven't looked closely at the patch yet,
but after VMD 1.9 is released I would be happy to dig into this and see
what the best way of accomplishing this will be.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 10, 2011 at 04:10:05PM +0100, Francesco Oteri wrote:
> Dear VMD developers,
> In the
> websitehttp://cmb.ornl.gov/resources/developments/top-patch-for-psfgen
> is reported a path to psfgen that permit to write a gromacs topology.
> I think that incorporating such a patch in the official distribuition
> could avoid wasting time if anyone needs to convert the psf file into
> gromacs topology.
>
> Best regards, Francesco 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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