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 - 14:21:18 CDT

PHS was Roux's primary hydration shell model
published a few years ago.

Carlos

----- Original Message -----
From: <rluo_at_uci.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, September 16, 2003 3:07 PM
Subject: Re: AMBER: MD simulations on small molecules immersed in sparse
water shell

> I don't know what PHS stands for. Do you mean the spherical boundary
> potential?
>
> In my PBMD simulations with shell waters. The restraining forces are
> turned on when the waters are 9 A away from the surface of the protein.
> This implementation is the same as the cap water setting except that the
> boundary surface is not a sphere (set to be 9 A away from the surface
> protein atoms).
>
> Since we have Langevin Dynamics now, stochastic forces are also applied
> to the waters to mimic the bulk. I believe this is the so-called
> generalized stochastic potential for arbitrary boundary though with
> long-range/reaction-field electrostatic correction taken care of by FDPB.
>
> Best,
> Ray
>
> Carlos Simmerling wrote:
> > 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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> >
> >
> >
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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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>

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