questions about accelerated MD

From: Thomas Evangelidis (
Date: Mon Sep 24 2012 - 09:46:30 CDT

Dear NAMD users,

I want to monitor the dynamics of a hetero-dimeric helical bundle in
complex with 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 in this regard:

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?

3. To save computation time I am thinking of applying a smooth force to the
backbone of the peptide that pulls it towards the COM of the binding site
whenever their distance exceeds a given cutoff value.

4. The protein dimer is long and thin and can fit into a parallepipedic
unit cell with one box vector long and the other two short. That type of
cell counts ~36 K atoms but the heterodimer tends to rotate and interact
with its periodic images. In contrast, when I fit the hetero-dimer into a
truncated octahedron I get a system of ~85 K atoms that slows down
calculations a lot. So I am thinking of applying a smooth force (TclForces
or TclBC) to rotate the helical bundle to bring it back into the box
whenever it sticks out.

I would be very interested to read you comments on these 4 points.

Thanks in advance,

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens


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