Re: AMBER: constant-pH MD with replica exchange

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Thu, 11 Oct 2007 14:30:34 -0400

why doesn't it work standard?
is there something other than energy needed for exchange
is it because the reps might have different protonation?

On 10/11/07, Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
> Maciek,
>
> We have been working on this, and will be sending a paper out next week
> for publication.
>
> Basically, Amber 9 cannot do this as distributed, but we hope to have
> the code in for the next release.
>
> Doing constant pH and replica exchange in pH space turns out to be
> inefficient in terms of sampling conformational space.
>
> So, what we do is to run constant pH MD doing REMD at different
> temperatures. Since the protonation state of a residue can be different
> in different temperatures, one needs to be very careful with the
> exchange equations, but it all works out ok.
>
> Adrian
>
>
> Maciej Dlugosz wrote:
> > Dear Amber developers/users:
> >
> > Is this possible to run constant-pH MD with
> > replica exchange?
> > Has anyone tried?
> >
> > Thanks,
> >
> > maciek
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department of Chemistry
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
> ============================================================================
>
> To announce that there must be no criticism of the president,
> or that we are to stand by the president right or wrong,
> is not only unpatriotic and servile, but is morally treasonable
> to the American public."
> -- Theodore Roosevelt
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>


-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 14 2007 - 06:07:27 PDT
Custom Search