VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Wed Nov 18 2009 - 02:20:38 CST

Hi!

Axel Kohlmeyer wrote:
> On Tue, Nov 17, 2009 at 12:15 PM, Ding, L. <ld82_at_leicester.ac.uk> wrote:
>> I was trying to generate a pdb file format. But the 200 pages of pdb file format introduction drive me crazy. Could someone here with polymer MD experience help me out?
>
> .pdb is a very bad file format for MD for a lot of reasons.
> actually .xyz isn't much better, since it requires to parse text files,
> which takes an enormous amount of time when reading
> long trajectory files.

I would recommend to have a look at the VTF/VSF/VCF file format family,
which I devised exactly for the purpose of self-written simulations:
http://espressowiki.mpip-mainz.mpg.de/wiki/index.php/VTF_trajectory/structure/coordinate_format

It is very easy to create such files from your own code, and you have
access to all visualization features of VMD. You *can* split your data
into topology and coordinate information, but you don't have to.

Olaf