From: Chiara Cardelli (
Date: Mon Apr 21 2014 - 04:21:58 CDT

I actually work with ORAC and I don't have
dcd files, just pdb files, but if I need them I'm sure I can convert them
somehow. Anyway, I know how to make a "normal" video with video maker, but
maybe I have to explain better which is the issue (I'm sorry if I wasn't
clear, I'm new in this mailing list and I'm still just a student).
In alchemical transformations the molecule which is "appearing" and
"disappearing" is actually always present in the coordinate files, so it is
visualized by vmd during the whole trajectory. But its potential
interaction with the surrounding is switched off at the beginning and then
gradually switched on, or viceversa, during the simulation. I would like to
see the molecule gradually appearing from invisible to transparent and then
visible, while the potential function is switching on. This doesn't happen
if I just press play, because the molecule is always there, altough it is
not interacting so it's like "invisible" for the rest of the system. Since
the alchemical transformations are implemented in NAMD, I was wondering if
such a visualization tool exists for VMD.

Thanks for helping,

2014-04-21 10:36 GMT+02:00 Fotis Baltoumas <>:

> 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,
> Fotis
> > 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
> >