From: Axel Kohlmeyer (
Date: Mon Apr 21 2014 - 11:18:16 CDT

On Mon, Apr 21, 2014 at 11:24 AM, Josh Vermaas <> wrote:
> Hi Chiara,
> The tools that work "out of the box" don't quite give you the level of
> detail you are interested in, since I assume you either want to change the
> radii by frame or the opacity by frame to give the illusion of
> appearing/disappearing. None of the default tools let you do this easily,

well, changing opacity in a material does often not give the desired effect.
an alternate approach would be to load the trajectory and create
two(!) visualizations, one for each of the two states.
then you run the moviemaker script on each of them but tell it to keep
the output and also change the template name in between. this way you
have now two sets of images.

now you can write a little shell script that combines the two images
with different transparency settings.

yet another alternative would be to create the two movies with VMD and
then use a video editing software to blend from one to the other
(might be the easiest option, if you have such a software readily


> however, with a bit of ingenuity, you can write your own script, as
> described in the vmdmovie plugin documentation
> (, which has an
> example on how to change the opacity towards the end. I've included a simple
> script that should work for changing the radii over your trajectory if you
> choose to do that instead.
> -Josh Vermaas
> set magicnumber 100 ; #Number of frames you want in total.
> set appearingsel [atomselect top "some atomselection text for the appearing
> atoms"]
> set disappearingsel [atomselect top "some atomselection text for the
> disappearing atoms"]
> set arad [$appearingsel get radius]
> set drad [$disappearingsel get radius]
> proc moviecallback { args } {
> global magicnumber
> global appearingsel
> global disappearingsel
> global arad
> global drad
> set frame $::MovieMaker::userframe
> animate goto $frame
> #Resize the radii. I'm trying to linearly interpolate from full size
> when it it fully present, to 0.1 when it is absent.
> $appearingsel set radius [vecscale [expr {0.1 + ((0.9 * $frame) /
> $magicnumber)}] $arad]
> $disappearingsel set radius [vecscale [expr {1.0 - ((0.9 * $frame) /
> $magicnumber)}] $arad]
> }
> proc enablemoviecallback { } {
> global magicnumber
> animate goto 0
> trace add variable ::MovieMaker::userframe write moviecallback
> set ::MovieMaker::numframes $magicnumber
> }
> proc disablemoviecallback { } {
> trace remove variable ::MovieMaker::userframe write moviecallback
> }
> On 04/21/2014 04:21 AM, Chiara Cardelli wrote:
> 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,
> Chiara
> 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
>> >

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.