From: Ashar Malik (
Date: Thu Dec 11 2014 - 20:58:14 CST

Hi there,

I am not aware of a way where this is possible (but I am not an expert
either). Also your query is a little unclear. Have you already done this
simulation? How did you do it? Conventional MD protocols require a
coordinate file and a structure file as starting points.

The PSF file must remain the same throughout the simulation. If you have
already conducted this simulation using an unconventional process and are
bent on using vmd to view ... You will have to view every change of system
separately ... What this means is that if you load a structure file ... And
a trajectory you can only visualize it till the number of atom changes in
the system. When an atom is added to the system, it changes the structure
file ( since that holds the number of atoms), when that changes that
basically means that its a new simulation ....

Hope that clarifies your query ... Also you should wait for someone else
(expert) to look at this post ...

Good luck,


On Dec 12, 2014 3:12 PM, "Jun-Chieh Wang" <> wrote:

Dear VMDers

I write a MD code to simulate deposition process.

In this simulation, Ar starts to deposit on

Si after a few hundreds of timesteps.

For example, for the first 100 timesteps,

only Si atoms (200 Si atoms) are in the simulation system.

After 100 timesteps,

Ar atoms kick in and start to bombard on the Si target.

As a result, the total number of atoms might be different

for each timesteps.

I output the position of each atoms for all timesteps

using xyz or vtf format.

It seems that xyz have to have the same number of atoms

for each timesteps,

so VMD cannot show the new Ar atoms

which enter the system later on.

VTF format also has the same problem.

Among all the formats that the VMD support,

which one should I choose if I have different total number

of atoms for each timesteps ?

Thank you.