VMD-L Mailing List

From: James Rustad (rustad_at_geology.ucdavis.edu)
Date: Thu Jul 06 2006 - 13:19:21 CDT

One code that will do this kind of thing is ECCE from Pacific
Northwest National
Lab, its free but you have to fax a registration form.
Ecce replaces the old XMOL functionality. Its odd
that xmol did this, and was written in the mid 80's.
Xmol was a real gem for ease of use with small systems.

Jmol is supposed to be a clone, but is not as convenient
in my experience. Ecce works very well.

Jim Rustad
jrrustad_at_ucdavis.edu

On Jul 6, 2006, at 10:56 AM, John Stone wrote:

>
> Hi,
> VMD will only load trajectories with a fixed number of atoms per
> trajectory timestep. If your XYZ file has a varying number of
> atoms per
> frame, VMD will not read it currently, and there's not really a
> workaround
> except to write them out as separate files and load them into VMD
> individually
> as separate molecules, animating them using scripts.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jul 06, 2006 at 11:00:52AM -0500, Jayendra Balasubramanian
> wrote:
>> I am trying to run an animation of an MD simulation in the xyz
>> format. The
>> number of atoms in each frame is different, however when I load
>> the xyz file
>> only the first frame shows up and vmd does not read the consequent
>> frames.
>> Is this because the number of atoms is different? How can this be
>> fixed?
>>
>>
>>
>> Jay
>>
>> Chemical Engineering
>>
>> UA
>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>