From: Anil Kumar (
Date: Mon Dec 10 2007 - 22:43:49 CST

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 Kumar
Research Scholar
Theoretical Sciences Unit
JNCASR, Bangalore
India -560064
Phone : 080-22082834
Mob. : 09342399856