I have a modified sander that applies the the cap restraining forces to
water molecules in such a setting.
Best,
Ray
Junmei Wang wrote:
>
>
>
>
> Dear AMBER users:
>
> I am running non-periodic boundary MD simulations for a set of middle-sized
> molecules (50-100 atoms). Each is immersed in a sparse water shell (10 to
> 20 TIP3P water, generated using solvateshell in LEAP). What is the best way
> to keep solvent molecules from drifting away from the solute along the MD
> simulations? This is no water cap information in the topology files if
> solvent molecules are added using solvateshell instead of solvatecap.
>
> Thanks
>
> Junmei
>
>
>
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> .
>
--
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528 Lab: (949)824-9562
Fax: (949)824-8551 e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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Received on Tue Sep 16 2003 - 19:53:00 PDT
