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?
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?
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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Received on Wed Sep 26 2012 - 11:30:04 PDT
