VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 12 2011 - 16:21:21 CDT

On Thu, 2011-05-12 at 21:04 +0000, Adkins, Laura R wrote:

laura,

> Axel,
>
> Thank you, this has resolved the issue, and I very much appreciate your help.

excellent. the changes and a couple of improvements that i noticed
on the side have been added to the VMD development version and will
be available on the next VMD release, too.

> For anyone hoping to use a similar technique, I'd like warn against
> using VMD to convert the input file to XYZ format, as I did. Similar
> to the unchanging atom names, the XYZ file formed has the same atom ID
> labels throughout the file, despite the input file having differing
> labels for different timesteps.

this is to be expected. what you are doing is not strictly speaking
a conversion, but you load the whole DL_POLY trajectory into VMD and
then save it in a different format. that means, all restrictions of
VMD do apply. if they wouldn't, then you could use DL_POLY files
right away in the way you expected to be able to use them. ;-)

cheers,
    axel.

> An XYZ conversion script is available in the DLPOLY utilities.
>
> Cheers,
> Laura
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.