From: Fotis Baltoumas (
Date: Mon Apr 21 2014 - 03:36:26 CDT

Dear Chiara,

I don't have any experience with alchemical simulations. However,
visualization of results can't be that different from visualization of
standard MD simulations. Therefore, if your simulation generates a DCD
trajectory file, you can visualize that in VMD by loading the original PSF
file as a new molecule and adding the dcd file as data.
You can have NAMD (I assume you work with NAMD) generate a trajectory for
your simulation by using the DCDfile option (and all other related ones)
in your NAMD configuration file. Then, simply use the Play button and the
"movie" of the simulation will commence.
If you want to make a movie (in AVI, quicktime or whatever) of the result,
there is a Movie Maker plugin in VMD.

Hope I helped,

> Is there any way in VMD to visualize an alchemical transformation? I mean
> like recording a video where a molecule is gradually disappearing
> somewhere
> (i.e. while its interaction potential with the surrounding is switched
> off)
> and contemporarily appearing somewhere else?
> Thank you,
> Chiara