AMBER Archive (2003)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Sep 16 2003 - 13:23:53 CDT

is this meant to be like Roux's PHS water model,
or does it work differently?
Carlos

----- Original Message -----
From: <rluo_at_uci.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, September 16, 2003 2:16 PM
Subject: Re: AMBER: MD simulations on small molecules immersed in sparse
water shell

> 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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