VMD-L Mailing List

From: B. Bennion (bbennion_at_u.washington.edu)
Date: Thu Oct 04 2001 - 00:47:08 CDT

Tom,

crd files work very nicely. This file is just a text file with three
columns of atomic positions, VMD does need to know how many atoms to put
in a single frame though. My group used crd files for awhile. An
intitial pdb file will give cmd what it needs to know.

your can access several file formats using the molecule menu.

Brian Bennion

 On 3 Oct 2001, tom
keyes wrote:

> Date: 3 Oct 2001 17:37:49 -0400
> From: tom keyes <keyes_at_chem.bu.edu>
> To: vmd-l_at_ks.uiuc.edu
> Subject: new user animation question
>
> Hello,
> I just got VMD running under OSX with Xtools, not Xfree86, and it seems
> fine so far. I'm a highly non-biological physical chemist simulating
> supercooled simple liquids and I want to animate MD trajectories. I usually
> write them as xyz for each atom, repeated for each time step in the same
> file. I added minimal PDB 'boilerplate' to a single configuration, gave it
> a .pdb extension, chose 'pdb only', and VMD displayed it nicely. I then
> saw the sentence in the User's Guide "...while PDB....files were designed
> to contain only one coordinate set, multiple files can be concatenated into
> one larger file to create a makeshift trajectory which is recognized by
> VMD." Thus I modified a FORMAT statement to add the pdb stuff to the xyz,
> and now I get a single pdb file repeated over and over in the same big
> file, differing only in xyz for each time step. However this did not work,
> VMD stalls on 'loading molecule'.
> So, am I on the wrong track? Do I need a different method of
> concatenation? Could someone provide more detail on what I quoted from the
> Guide? I've found a script 'animatepdbs' which apparently will animate a
> sequence of distinct pdb files, one for each config, and it will be trivial
> to write a lot of little files instead of one big one, or I suppose it
> could be modified to pick the date for one time step out of the big file.
> However what i tried first seems simplest. Can something like that work?
>
> Thanks
> Tom Keyes
>
>
>

Graduate Research Assistant
Dep. Medicinal Chemistry, University of Washington
Tel# (206)616-2779
BOX 357610 Seattle WA 98195

email--bbennion_at_u.washington.edu
web page--http://students.washington.edu/bbennion