AMBER Archive (2004)

Subject: Re: AMBER: question on simulated annealing

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 28 2004 - 11:24:59 CDT

On Wed, Apr 28, 2004, Venkata S Koppuravuri wrote:
>
> 1. Is it a general procedure to do simulated annealing in vacuum ??

In "modern" calculations, people would be more likely to use a generalized
Born force model than a vacuum one, but the principles are the same.

>
> 2. Is it also possible to do it with a solvent like water ?? If possible
> can someone tell me where I can find an example for that.
>

This is possible, but the actual heating and cooling schedules would have to
be quite different. If you are using simulated annealing as an optimization
procedure, there are some problems involved with trying to cool a solvated
system down to 0K. You will get stuck in a glassy-like liquid state that is
probably not very relevant to your real physical problem.

...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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