[AMBER] How to choose the boost for aMD when using restraints

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Tue, 15 Jan 2013 22:32:35 +0200

Greetings,

I want to monitor a peptide-protein interaction with dual-boost aMD using
coordinate restraints on some atoms of the protein and flat-well restraints
on the peptide to keep it close to the binding site. In the cMD that I will
run at the beginning to estimate the aMD parameters, should I activate
those restraints or not?

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 Tue Jan 15 2013 - 13:00:03 PST