Re: [AMBER] acclerated molecular dynamics alphaP

From: Daniel Roe <>
Date: Tue, 29 Oct 2013 09:19:58 -0600


The overall potential boost is applied to the entire system, so if
you're determining alpha based on the recommendation of Hamelberg et
al.(alpha ~ Ethreshold - Vmin) you should use Ethreshold and Vmin
from the potential energy of the entire system. Of course this is a
recommendation rather than a rule; you may need to play around with
the exact value.


On Tue, Oct 29, 2013 at 8:59 AM, Nicole Ippolito
<> wrote:
> Hello,
> I have a general question. When calculating alphaP for acclerated MD, do
> you use the total number of atoms in the pdb (counter ions and waters
> included) or is it just the atoms in the protein? I am assuming it is the
> total atoms in the pdb, but I just want to clarify this.
> Nicole Ippolito
> Auburn University
> _______________________________________________
> 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 Tue Oct 29 2013 - 08:30:06 PDT
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