VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Wed Nov 18 2009 - 06:48:36 CST

Another alternative is to use the stand-alone XTC library from Gromacs, which is lightweight and independent of any larger code:
http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library

I've used it in a couple of applications that I've written, and it works well.

Josh

On Nov 18, 2009, at 3:20 AM, Olaf Lenz wrote:

> 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