Re: [AMBER] Finding a good REMD temperature ladder

From: Daniel Roe <>
Date: Wed, 9 Jul 2014 13:47:16 -0600


Out of curiosity, in your replica log at the very last exchange do you see
a corresponding dip in exchange acceptance between replicas 55 and 56?

On Wed, Jul 9, 2014 at 12:01 PM, Eugene Yedvabny <>

> but for some reason there's almost no exchange between the two groups. The
> behavior suggest there's little overlap between the 55th and 56th replica's
> energy distributions, but I can't rationalize why that would be the case
> for that particular temperature pair.

Have you looked at the PE overlaps to verify this? It's certainly not out
the realm of possibility that there is a bug in remlog analysis itself
(although I really hope not)...


PS - Are each of these both from single runs (i.e. one remlog) or from
multiple runs strung together?

> Has anyone seen this kind of behavior in REMD simulations using a ladder
> from the online calculator? Any suggestions on how to increase the mixing
> rate and break that barrier would be greatly appreciated! If you also have
> links to other suggested REMD temperate calculators I'd be happy to give
> them a try.
> Thank you,
> Eugene Yedvabny
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jul 09 2014 - 13:00:03 PDT
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