Re: How to do a rigid solvent model?

From: David A. Case <>
Date: Fri, 4 Jul 2003 10:16:51 -0700

On Fri, Jul 04, 2003, Marco Aurelio Correia Preto wrote:
> We are doing some molecular dynamic runs of small non-standart peptides (in
> water) and we would like to do the smae dynamics in other solvents! There
> are a couple of potential for organic solvents, but some of them are rigid
> one! How can we do this in Amber (version 6 is the one we have)? Can we use
> very large force constants to force a rigid conformation?

It is more typical to use SHAKE to keep solvent molecules rigid. Some other
solvents (chloroform, methanol, acetonitrile, ...) are available at:

...good luck...dac
David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Fri Jul 04 2003 - 18:53:00 PDT
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