Subject: MD with water ...

From: [email-masked] (Pieter Stouten)
Date: Fri, 27 Aug 1993 15:41:44 -0500

On Fri, 27 Aug 93 13:37, Arne Elofsson <[email-masked]> wrote:

>the solvent effect can be reproduced
>rather well with specific solvent potentials but
>they seem to be slower than to include specific
>waters. (Chris Sander had a paper in last J.M.B  
>with something that sounded very fast.)
>
I am not completely sure, but somehow doubt that it was published in
J.M.B. :-). Also, effective solvation can be much faster than using
explicit water. Our method is only 20-50% (20% in PRESTO, 50% in
GROMOS) slower than VACUUM simulations.

The reference is: P.F.W. Stouten, C. Froemmel, H. Nakamura & C. Sander,
"An Effective Solvation Term Based on Atomic Occupancies for Use in
Protein Simulations," Mol. Simulation 10 (1993) 97-120.

Cheers, Pieter.

Pieter Stouten, Senior Research Scientist    ||
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