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

From: Carlos Simmerling <carlos.csb.sunysb.edu>
Date: Tue, 16 Sep 2003 14:23:53 -0400

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

----- Original Message -----
From: <rluo.uci.edu>
To: <amber.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
> >
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
> > .
> >
>
> --
> ====================================================
> 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/
> ====================================================
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Sep 16 2003 - 19:53:00 PDT
Custom Search