Re: MOE program and difference between MD and SA?

From: Brian Bennion (
Date: Fri Nov 14 2003 - 10:35:15 CST

Moe is a very expensive package that cannot be downloaded.
unfortunately I have not found a free linux based molecule editor, there
is a free windows molecule editor from arguslabs in Seattle; search for
arguslabs to find it.

Simulated annealing is not molecular dynamics per se. In SA you heat
system to very high temperatures and slowly cool while using MD. This
process is generally only used for small molecules because a protein would
blow apart and never come back together again in age of the universe.


 On Fri, 14 Nov 2003, wrote:

> Dear Sir,
> (1) I read a lecture in the NAMD homepage on how to determine force field for new
> molecule or ligand.However it says MOE program is need. Whether does anyone know
> where I can download this program?
> (2) I find a problem about Namdplot script on the NAMD utilities. I can't see any
> figure with this namdplot script. When I modify the line 150:
> grep '^ENERGY:' $argv | grep -v '[a-z]' | awk "$prog" > $tmpfile
> to:
> grep '^ENERGY:' $argv | awk "$prog" > $tmpfile
> it can work.
> Is my modification right?
> (3) When I read some books, I see a expresssion"Simulated annealing". It should
> belong to a molecular dynamic simulated method. What are the difference between
> "MD" in NAMD program and "Simulated annealing"?
> Thank you very much!

**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 422-6605                 **

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