From: Chiara Cardelli (chiaracardelli88_at_gmail.com)
Date: Tue Apr 22 2014 - 04:19:29 CDT

Thank you very much for helping I`m trying those options.

Chiara

2014-04-21 18:18 GMT+02:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:

> On Mon, Apr 21, 2014 at 11:24 AM, Josh Vermaas <vermaas2_at_illinois.edu>
> 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
> available).
>
> axel.
>
>
> > 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>:
> >>
> >> 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 akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>