VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Apr 21 2014 - 10:24:57 CDT

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, however, with a bit of ingenuity, you can write your own script,
as described in the vmdmovie plugin documentation
(http://www.ks.uiuc.edu/Research/vmd/plugins/vmdmovie/), 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 http://www.chim.unifi.it/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 <fbaltoumas_at_biol.uoa.gr
> <mailto:fbaltoumas_at_biol.uoa.gr>>:
>
> 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
> >
>
>
>