From: Norman Geist (
Date: Fri Dec 12 2014 - 02:43:08 CST



You face a general problem here. You will not be able to load trajectories of different atom count into the same molecule in VMD. But assuming that the atom count stays the same for some amount of time, your code should write individual trajectories every time the atom count changes.

Now write a TCL script that loads each of these trajectories to VMD as individual molecules, but create empty fake frames (all coordinates -100 or so; display reset view will not work fine than) before you actually load the real trajectory since the 2nd molecule. In that way you will still be able to use the play function of VMD and it will look like the atoms appear like normal.


Example (-=real frame; *=fake frame)


Mol 0 -------*******************

Mol 1 ******------------*********

Mol 2 ****************-----------


You could also use “trace” to trigger changes of the animation frame to show/hide molecules based on if they currently have fake frames or not.


Good luck.


Norman Geist.


Von: [] Im Auftrag von Ashar Malik
Gesendet: Freitag, 12. Dezember 2014 03:58
An: Jun-Chieh Wang
Betreff: Re: vmd-l: format I should use if I have different total number of atoms for each timesteps


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.