Fwd: 99999999.9999 as vander waals energy

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Sat Jul 11 2009 - 19:38:30 CDT

It means you have a high-energy vdW interactions, likely a "near clash" of
two different atoms in multiple sites through your system. Minimization, if
ran long enough, should clean these up in most reasonable cases and permit
you to proceed to equilibrate your system with MD. You should continue
minimizing until your energies are converged, exhibiting little to no net
change over many steps; only fluctuations about a mean value.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
Fax: 217-244-6078
On Sat, Jul 11, 2009 at 12:18 AM, Uma Mageshwari
> Hello,
>        I am trying to do a simulation using Namd. During minimisation i am
> getting 99999999.9999 as vander waals energy at first step. But later its
> decreasing.......
>                         1.Does it mean the error in peridic boundary
> condition?
>                         2. Could it affect the result?

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