RE: visualizing dynamics output

From: Samuel Flores (samuel.flores_at_yale.edu)
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

Sam

-----Original Message-----
From: Brian Bennion [mailto:brian_at_youkai.llnl.gov]
Sent: Tuesday, March 22, 2005 1:55 PM
To: Samuel Flores
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: visualizing dynamics output

Have you heard of VMD? www.ks.uiuc.edu/Research/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.

Brian

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
errors.
> 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
>
>

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