From: Axel Kohlmeyer (
Date: Thu Nov 07 2013 - 16:34:13 CST

On Thu, Nov 7, 2013 at 10:37 PM, Leonhard Henkes
<> wrote:
> Dear VMD users,
> I would like to ask if there is a way to run a VMD Tcl script during an
> interactive MD run in NAMD and how it should or could be implemented ? For
> demonstration and lecturing, I setup a small system with two graphene
> sheets and a C60 ball. Now I would like to to change the color/material of
> a molecule and draw some text on the VMD screen, if a trigger point is
> passed.
> However I tried to add some VMD commands (atomselect, measure etc.) to my
> NAMD config, which didn't work. I also tried to add my conditionals into

no. this doesn't make any sense anyway.

> the VMD script, which manages the synchronization and representation by an
> for the IMD, but I couldn't manage to update my script for each frame
> during the IMD run.

there are probably better ways to do it, but you should be able to set
a trace on vmd_frame($mol). if needed, you can just set up IMD to
record frames (very infrequently) and then you can use the frame count
as a time code.


> Thanks for your help and ideas,
> Leo

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.