VMD-L Mailing List

From: Ardy Davari (ardydavari_at_gmail.com)
Date: Tue Jul 06 2010 - 09:30:27 CDT

Hi,

I am not sure if this will work, but I have a separate trajectory file with
velocities stored inside it. (I used a vv2 integrator and the parameters
nsavv 100 and iunv to do this. )

Is it possible to extract the velocities from those files in vmd?

-Ardy

On Tue, Jul 6, 2010 at 3:51 AM, Bjoern Olausson <namdlist_at_googlemail.com>wrote:

> On Monday 05 July 2010 22:59:22 Ardy Davari wrote:
> > Hi,
> >
> > Are there any scripts available to color a charmm dcd/psf by kinetic
> > energy?
> >
> > If not, what's the best way to go about producing one?
> >
> Since the energy is not stored in the dcd you have to either calculate it
> or
> get it elsewhere.
>
> If you want to color it by the TOTAL energy you could simply grep the TOTAL
> (TOTAL2, TOTAL3) from the NAMD log file for every frame and write it to a
> file
> (You might want to check the build in extension "NAMD Energy"). Then write
> a
> little script that colors every frame of you dcd by a certain color
> depending
> on the TOTAL energy.
>
> set sel [atomselect top "all"]
> for {set i 0} {$i < $maxFrames} {incr i} {
> $sel frame $i
> $sel set user $YourEnergyRepresentationValue
> }
>
> I don't know how to read in an external file but I am sure someone else
> does,
> or you can figure it out by yourself.
>
>
> Hope this helps.
>
> Cheers
> Bjoern
>
> --
> Bjoern Olausson
> Martin-Luther-Universität Halle-Wittenberg
> Fachbereich Biochemie/Biotechnologie
> Kurt-Mothes-Str. 3
> 06120 Halle/Saale
>
> Phone: +49-345-55-24942
>