AMBER Archive (2003)

Subject: Re: AMBER: MD simulations on small molecules immersed in sparse water shell

From: rluo_at_uci.edu
Date: Tue Sep 16 2003 - 13:16:41 CDT

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_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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