VMD-L Mailing List

From: Mauricio Carrillo Tripp (tripp_at_fis.unam.mx)
Date: Tue Oct 09 2001 - 20:01:20 CDT

> Hi,

I tried the PDB+CRD trick to view an animation of a MD and it works great,
although
i noticed that i have to put a blank line at the biggining of the CRD file in
order for it
to work properly (bug? or i'm missing some info?). I also noticed that the %CPU
goes to
the top whenever i create a 'graphics' object (using the "draw" command) and
goes back
to normal when i delet the object, is this normal? I'm using VMD 161/RedHat7.1
Going back to the animation question, it would be very helpful if I could show
the behavior
of the energy as the simulation evolves, this way I could easylly detect
structures of
interest any time the energy jumps or does something in particular, is there any
way
to do this?
TIA

Mauricio C. Tripp
Biophysics Department
CCF-UNAM
México

>
>
> On Thu, Oct 04, 2001 at 10:44:41AM -0400, tom keyes wrote:
> > On Thu, Oct 4, 2001 1:47 AM, B. Bennion <mailto:bbennion_at_u.washington.edu>
> > wrote:
> > >crd files work very nicely. This file is just a text file with three
> > >columns of atomic positions, VMD does need to know how many atoms to put
> > >in a single frame though. My group used crd files for awhile. An
> > >intitial pdb file will give cmd what it needs to know.
> > >
> > >your can access several file formats using the molecule menu.
> >
> > Brian,
> > Thanks, it would be very convenient to be able to use a text file with 3
> > cols xyz, my usual way of writing trajectories. However all I find in the
> > Molecule menu using crd is parm and crd. How do you load pdb and crd? If I
> > figure out how to write a parm file can I just load it plus my trajectories
> > renamed .crd?
> > BTW I said yesterday VMD choked on loading a big file of repeated pdb
> > files for different time steps. When I made the file smaller by taking just
> > a few time steps it read it but said it was one frame with more atom, the
> > number of atome = the true number times the number of time steps.
> > Tom
> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
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