AMBER Archive (2003)

Subject: Re: SANDER vs GIBBS equilibration

From: David A. Case (case_at_scripps.edu)
Date: Thu Mar 27 2003 - 14:44:08 CST

On Wed, Mar 26, 2003, Sophia Kondratova wrote:

> I have noticed something peculiar while trying to perform an FEP
> simulation of phenol --> benzene in gas phase using the GIBBS module
> of AMBER7.

Sounds like something is wrong. You have to be careful about
"equilibration" of a small, almost rigid gas phase molecule. There is really
nothing it should be able to do, and therefore nothing to equilibrate. But
since there are so few degrees of freedom, the notion of a "temperature"
can be tricky. Check the total energy is being conserved. The mean
potential energy should be the same in sander and gibbs.

Take a visual look at the system to make sure it looks like phenol, etc.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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