Hi Thomas
I added comments to your questions bellow.
> Dear Amber users,
>
> I want to monitor the dynamics between a hetero-dimeric helical bundle
and
> a peptide. It is believed that the peptide binds at the protein-protein
interface of the dimer and unwinds the helix of one of the components.
For
> this purpose I am considering accelerated MD (aMD) but have some queries
about it:
>
> 1. Unlike Metadynamics, the bias in the potential is not history dependent,
> therefore the system may explore multiple times the same area of
conformational space. Is this correct?
This is correct, AMD will make it more probable to move out of deep stable
basins in the conformational space and there is no mechanism to prevent it
from going back.
>
> 2. Is it possible to find the predominant conformations of the complex from
> an aMD trajectory, namely the ones that we would expect to observe the most
> in an unbiased MD trajectory?
Yes, what you will get in the end of the AMD calculation is a state
distribution, that although is not the unbiased (canonical) one, it still
holds some resemblance to it. AMD distributions can be re-weighted to
produce Boltzmann distributions.
Please refer to these papers for more information.
(a recent paper we just published on the GPU implementation of AMD)
http://pubs.acs.org/doi/abs/10.1021/ct300284c
(one of the main papers for this method)
http://www.cse.nd.edu/~izaguirr/HaMM04.pdf
I hope this helps, let me know if you need more information.
Best,
Romelia
>
> I would be grateful if someone could give me some answers.
>
> Thanks in advance,
> Thomas
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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--
****************************************
Romelia Salomon
Walker Group
398 San Diego Supercomputing Center
UC San Diego
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Received on Wed Sep 26 2012 - 15:30:03 PDT
