Dear Dan,
Thank you for your (speculative) reply. Sometimes it is good to know that the answer is either unclear or unknown.
The only thing I was unclear about in your explanation is the effect of this selective boost (" ... if the average energy of your "folded" conformation lies below the boost energy threshold and the average energy of your "unfolded" conformation lies above it ...").
Would this, in practical terms, imply that the folded structure is likely to be overrepresented in the trajectory, or do I have this concept the wrong way round?
Best wishes,
Robert
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] accelerated MD - frequency of conformational
change
To: AMBER Mailing List <amber.ambermd.org>
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Hi,
To my knowledge I don't think this is a question that has been looked
into in great detail (others please correct me if I'm wrong). My
intuition tells me that aMD can certainly alter kinetics in a
non-symmetrical way, particularly if your boost energies are being
applied only on one "side" of a transition. For example, if the
average energy of your "folded" conformation lies below the boost
energy threshold and the average energy of your "unfolded"
conformation lies above it, then the energy landscape is altered only
for your "folded" conformation which will certainly affect the
kinetics between folded and unfolded with respect to the unaltered
energy landscape.
Big disclaimer: this is just what I think based on my experiences with
aMD. Hopefully it's useful.
-Dan
On Fri, Feb 5, 2016 at 10:54 AM, Weinzierl, Robert O J
<r.weinzierl.imperial.ac.uk> wrote:
> Dear Amber Users,
>
> During the course of an accelerated MD (aMD) of a small peptide I observed the formation/dissolution of an alpha-helix at a particular frequency. Is it possible to deduce from such aMD data that the frequency of (reversible) conformational change would be similar if the simulation was run without any acceleration? Or does aMD change the kinetics so substantially that the relative proportions of time spent in the folded and unfolded state would be quite different in "real time"?
>
> The aMD simulations were run as specified in the Amber manual with the recommended alpha factor of 0.2.
>
> ROJW
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Received on Sun Feb 07 2016 - 03:30:03 PST
