VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 04 2008 - 12:38:08 CST

Hi,
  VMD doesn't presently allow atom types to change during the course
of a trajectory. Rather than labelling the atoms by changing their
atom types, you can set a flag in one of the per-timestep "user" fields.
VMD will then allow you to select/color/display the atoms by this
time-varying property. You can set this field using a Tcl script.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 10, 2007 at 09:42:58AM +0530, Anil Kumar wrote:
>
> Dear all,
>
> I want to make a movie, in VMD, of a trajectory(xyz coordinate file)
> which is obtained from MC simulation. Trajectory file has two type of
> atoms (say A and B). Initial configuration has 10% of A atoms and 90% of B
> atoms. During the simulation number of A type atoms increases and number
> of B type atoms decreases. Final configuration has say 80% of A and 20% of
> B atoms.
>
> 1. Now I have given two elemental name for A and B atoms (say Ar & Na).
> When I visualize this file in VMD. Then color code it shows only from the
> initial configuration(I mean 10% of particles have color A and 90% of
> particles have color B.) But it can't visualize the way the number of A
> particles have increased during simulation.
>
>
> 2. Also, If I take only A type of Atoms in my trajectory file, so this
> trajectory file contains different number of Atoms in different frame(As
> number of A type atoms increases during simulation). VMD can't visualize
> this file.
>
> Could you please help me how to visualize above both type of trajectory
> in VMD.
>
>
> Thanking you in anticipation.
>
> With Best Regards,
> Anil
>
>
>
>
>
>
>
>
> 

-- 
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