Thank you so much Dr. Simmerling.
Tarique
----- Original Message -----
From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
To: "Syed Tarique Moin" <tarisyed.yahoo.com>, "AMBER Mailing List" <amber.ambermd.org>
Sent: Monday, 8 April, 2013 11:39:17 PM
Subject: Re: [AMBER] implicit solvation with periodic boundary
there are various ways one could do this, but I would probably use a
distance restraint between the centers of mass of the two groups. the
details of how to define the flat region and the region with penalty
are described in the manual.
===================================================================
Carlos Simmerling, Ph.D.
Professor, Department of Chemistry
Associate Director, Laufer Center for Physical and Quantitative Biology
Laufer Center, Room 119 Phone: 1-631-632-5424
Stony Brook University E-mail:
carlos.simmerling.stonybrook.edu <carlos.simmerling.gmail.com>
Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
===================================================================
On Mon, Apr 8, 2013 at 5:27 PM, Syed Tarique Moin <tarisyed.yahoo.com>wrote:
> Thank you, Jason and Carlos. Can you please guide me a bit about "flat
> well distance restraint to enforce a specific
> concentration in a spherical volume". Is it used with implicit solvent and
> how?.
>
>
> Tarique
>
> ----- Original Message -----
>
> From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Cc: "Syed Tarique Moin" <tarisyed.yahoo.com>
> Sent: Monday, 8 April, 2013 10:28:20 PM
> Subject: Re: [AMBER] implicit solvation with periodic boundary
>
> I agree with Jason, but one effect is that you have infinite dilution. For
> binding, you could use a flat well distance restraint to enforce a specific
> concentration in a spherical volume.
> On Apr 8, 2013 4:13 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
> >
> >
> > On Apr 8, 2013, at 10:39 AM, Syed Tarique Moin <tarisyed.yahoo.com>
> wrote:
> >
> > > Hello,
> > >
> > > I am interested to simulate a protein in implicit solvent with periodic
> > boundary condition. Can someone suggest me is it possible in Amber.
> >
> > No. This is a highly unusual calculation. Periodic boundary conditions
> are
> > used to avoid surface effects in explicit solvent simulations. Since
> > implicit solvent simulations do not have solvent boundaries (the
> continuum
> > goes on forever), there is rarely a reason to use periodic boundary
> > conditions.
> >
> > Good luck,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> >
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> >
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Received on Mon Apr 08 2013 - 17:00:02 PDT
