VMD-L Mailing List

From: Suman Chakrabarty (suman_at_sscu.iisc.ernet.in)
Date: Tue Mar 04 2008 - 15:19:58 CST

Dear all,

I have just started using VMD for some visualization of simple
Lennard-Jones fluid systems. I am facing some problems to do the following:

My system consists of only two types of atoms (Lennard-Jones particles):
A and B. Their identities can interchange. So, the number of A and B
changes during the simulation. In some cases even the total number is
not constant, i.e. some particles can diseapear from the system.

I want to visualize the trajectory of only A type atoms throughout the
simulation.

Since I am new to file formats, I am using simple XYZ format as follows:
total number of A type atoms in the system in the first line followed by
an empty line and then coordinates like "H x-coord y-coord z-coord"
(let's say the A type to be Hydrogen). Different frames will be appended
one after another, with changing number of particles at every frame.

Even the "Update Selection Every Frame" option is not serving the
purpose (if I have correctly understood the purpose!). It always assumes
the number of particles given at the first frame!

Please help me to achieve this goal using VMD. I can provide further
information regarding my system if needed.

Thanks,
Suman Chakrabarty. 

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