VMD-L Mailing List

From: David Kingsbury (trentdk_at_gmail.com)
Date: Sun Jul 24 2005 - 23:39:25 CDT

http://newton.cofc.edu/surf2005/media.htm
The latest movie is done using VMD and that script.

(please note, in my previous post, the $file is supposed to be $pdb_file)

On 7/24/05, David Kingsbury <trentdk_at_gmail.com> wrote:
> Thanks for the help axel and blake!
>
> I had no idea about the User field until your reply. Then, after some
> reading about the "atomselect" function and such, I modified this
> sample script I found on the mailing list. I'm using your idea of
> reading in the KE values from another file ( I couldn't read from the
> beta field, even though i would specify a different frame.. it still
> retained the frame 1 values). The ke file is just a long list of ke
> for each atom, and each frame is cancatinated to the file. This
> script then applies each ke to each atom, frame after frame. Works
> great!
>
> Btw.. awesome website Axel! I'll send ya a link to some movies of
> this stuff when i get it up. Its c60 bombarding si crystal. Beautiful
> stuff =D
>
> Here is the script!
> #---------------------------------------------------
>
> set pdb_file H:/sput/run/c60si.pdb
> set ke_file [open "H:/sput/run/c60si.ke" r]
>
> if {[molinfo num] > 0} {
> mol delete all
> }
>
> mol addfile $file waitfor all
>
> set numframes [molinfo top get numframes]
> set numatoms [molinfo top get numatoms]
>
> mol modcolor 0 top User
> mol colupdate 0 top 1
> mol scaleminmax top 0 0.0 20.0
>
> for {set i 0} {$i<$numframes} {incr i} {
>
> animate goto $i
> puts "Setting User data for frame $i ..."
>
> for {set j 0} {$j<($numatoms)} {incr j} {
> set ke [gets $ke_file]
> set atomsel [atomselect top "index $j" frame $i]
> $atomsel set user $ke
> $atomsel delete
> }
> }
>
> #-------------------------------------------------
>
> On 7/24/05, Axel Kohlmeyer <axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de> wrote:
> > On Sat, 23 Jul 2005, David Kingsbury wrote:
> >
> > hi dave,
> >
> > DK> I'm running some MD simulations and want to have an on-the-fly
> > DK> coloration of KE. I thought it would be ingenius to place the KE
> > DK> values into the BETA field of a .pdb file, and watch it with VMD. So
> > DK> now I have a 10 frame .pdb file of some action where the ke in the
> > DK> beta field is changing every frame. I made sure to color by BETA, and
> > DK> to check the "update color every frame" in the trajeectory tab. VMD
> > DK> however is not updating the colors... it is just retaining frame 1's
> >
> > yep, that is how the VMD works. all structure and other similar
> > information (bonds etc.) are only taken from the first frame
> > (or a supported topology files) and from the remaining frames
> > only the coordinates are taken.
> >
> > DK> BETA coloring scheme. Does anyone have any suggestions to get this
> > DK> working? I have a feeling it my be a small fix, (or a bug?)
> >
> > there are actually two ways to this (been there, done it, and got the
> > t-shirt ;-) ). either you store the data in the 'user' field (which
> > is per frame, unlike beta) and use the 'User' colorization scheme
> > or write a small function to be hooked into the animation loop
> > that updates the beta field according to your pre-calculated values.
> >
> > please have a look at:
> > http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect3
> > for an example of the first method and about one screen down at:
> > http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect4
> > for an example of the second method.
> >
> > in your case, you probably want to use the first method, but
> > then read the data from a separate file, like in the second example.
> >
> > i also should have a VMD script example somewhere, that computes
> > an estimate of the instantaneous kinetic energy from within VMD
> > (from distance differences) and stores it directly into the user
> > field. unfortunately, i did not have the time to add it to
> > the tutorial pages yet, so let me know, if i should send it to you.
> >
> > regards,
> > axel.
> >
> > DK> Thanks!
> > DK> -David B. Kingsbury
> > DK> College of Charleston
> > DK>
> > DK>
> >
> > --
> >
> > =======================================================================
> > Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> > Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> > D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> > =======================================================================
> > If you make something idio
> t-proof, the universe creates a better idiot.
> >
> >
>
>
> --
> -David Kingsbury
> 

-- 
-David Kingsbury