VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Apr 26 2010 - 15:01:16 CDT

On Mon, 2010-04-26 at 15:59 -0300, Diego Javier Alonso de Armiño wrote:
> Hi everybody!
>
>
> I'm performing some QM-MD simulations of a small inorganic molecule
> using GAMESS. But GAMESS' trajectory files are unsupported by VMD.
> Obviously it would be wonderful if I could count with vmd for the
> analysis of results. So I was thinking that given that I have some
> knowledge of Perl scripting, maybe I could convert gamess trajectory
> files to something VMD can recognize. Despite some digging, though, I
> couldn't figure out which format would be most convenient to convert
> it to, as all seem to require the specification of a set of parameters
> (which are irrelevant in a quantum mechanical simulation).

no. those parameters are not really needed.
if you are willing to do some programming, you could just
write a molfile plugin, perhaps based on the xyz plugin,
as that is the absolute lowest common denominator.

> Can anyone recommend a curse of action? Is there any trajectory format

i really don't want to recommend a curse. ;)

but there are a number of possible courses:
- write a molfile plugin. that would be the the most programming but
  result in the fastest reading.
- write a parser in tcl (or python?) and generate the trajectory
  in VMD itself. you can have a look at the topotools plugin for
  a number of examples, most notably parsing the LAMMPS data file
  format. but also for .xyz. may be less effort to write, but
  parsing in tcl is slower.
- write a converter to some simple text format (e.g. .xyz) and import
  that. requires double the disk storage and text file parsing is slow.
- modify the GAMESS so that i writes the trajectory directly in the
  preferred format and then just generate a "fake" .psf file with
  the missing information. i've done this with CPMD for example by
  implementing .dcd format output, which allows fast reading of
  long trajectories.

> that doesn't require the specification of a parameter set? If not, Is
> there a way to generate a valid prmtop file (in the case of Amber
> format) for a QM MD run?

amber format is quirky to say the least. prmtop is one of the few
formats that encodes parameters into the topology. not sure if the
corresponding parser in VMD can handle it, if you don't provide them.
their advantage is that they encode the format of the data that is
following. .psf files require a more careful/rigid output formatting,
but are structured much simpler.

cheers,
   axel.

>
> Thank you very much for your valuable time! And greetings from
> Tucumán, Argentina
>
>
> Diego Javier Alonso de Armiño
>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.