RE: visualizing dynamics output

From: Michel Espinoza-Fonseca (
Date: Tue Mar 22 2005 - 14:17:12 CST

When you load the out.coor, it is better if you ask the NAMD to write
the output file in plain text (not binary), and then it'll be much
better for you to transport and handle your file using other programs.
Try to load the binary (if it is your case) .coor file + the psf file.
But again, my advice is to write the output.coor NOT as a binary.

Hope it works :)

-----Original Message-----
From: [] On
Behalf Of Samuel Flores
Sent: Tuesday, March 22, 2005 1:51 PM
To: 'Brian Bennion'
Subject: RE: namd-l: visualizing dynamics output

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
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
> 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
> motion of the protein in its water sphere. Is there some way to do
> 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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