VMD-L Mailing List

From: Jun-Chieh Wang (wangjj0120_at_gmail.com)
Date: Thu Dec 11 2014 - 19:47:04 CST

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.