RE: visualizing dynamics output

From: Samuel Flores (
Date: Tue Mar 22 2005 - 13:51:07 CST

Yes, I've heard of VMD. However when I execute vmd outputfile.coor I get a
blank screen. This was not the case when visualizing pdb's. Is there some
special procedure to be done to make this molecule visible?

Many thanks


-----Original Message-----
From: Brian Bennion []
Sent: Tuesday, March 22, 2005 1:55 PM
To: Samuel Flores
Subject: Re: namd-l: visualizing dynamics output

Have you heard of VMD?

it goes hand in hand with NAMD

The high energies are a result of poor boundary conditions, mistakes in
topology files or problems in psfgen with psf file is created.


On Tue, 22 Mar 2005, Samuel Flores wrote:

> Howdy all,
> Many thanks for past help getting set up on NAMD! I have successfully
> completed a few test runs. On a certain protein I try to run, I get very
> high energies (sometimes maxing out at 99999999) but no warnings or
> In order to diagnose what's going wrong, I think I need to visualize the
> motion of the protein in its water sphere. Is there some way to do this?
> Sam

  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605

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