From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Mar 22 2005 - 12:55:00 CST
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
>
>
************************************************
Brian Bennion, Ph.D.
Bioscience Directorate
Lawrence Livermore National Laboratory
P.O. Box 808, L-448 bennion1_at_llnl.gov
7000 East Avenue phone: (925) 422-5722
Livermore, CA 94550 fax: (925) 424-6605
************************************************
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:16 CST