VMD-L Mailing List

From: radak004_at_umn.edu
Date: Mon Apr 26 2010 - 16:38:36 CDT

I'm pretty sure there are several supported trajectory formats that do not
require a .prmtop type file. My personal favorite (i.e. the only one that I
really know) is .xyz, which is simple enough, but not particularly space
efficient (as opposed to any of the binary formats).

You can probably find more info elsewhere, but the general format is:

<number of atoms in the system>
<blank line or comment line (sometimes the time step)>
<atom type> <x coordinate> <y coordinate> <z coordinate>

etc. etc. (this would repeat for each time step, so the number of atoms is
redundantly listed). I can see it being quite easy to write a script to
convert an arbitrary, but known, file type into this format.

Maybe that helps?
Brian

On Apr 26 2010, 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).
>Can anyone recommend a curse of action? Is there any trajectory format 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?
>
>Thank you very much for your valuable time! And greetings from Tucumán,
>Argentina
>
>Diego Javier Alonso de Armiño
> 

-- 
Brian Radak
University of Minnesota - Twin Cities
Dept. of Chemistry and Chemical Physics
Teaching Assistant, CHEM 1021/1022/8551
Graduate Student, York Research Group
65 Kolthoff Hall
207 Pleasant St. SE
Minneapolis, MN 55455
radak004_at_umn.edu
(612) 625-6317 (office)
(612) 626-7541 (fax)