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
> >
> >
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>
> --
> 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
> ============================================================================
>
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Received on Sun Oct 14 2007 - 06:07:27 PDT
