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
--
==================================================================
David A. Case | e-mail: case.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:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Mar 27 2003 - 20:53:01 PST
