Re: accelerated MD new variant

From: Brian Radak (
Date: Mon Nov 30 2015 - 09:48:36 CST

I don't believe that aMD is being actively developed at the moment.
Although the Hamelberg paper is not the only variation in the past few
years, so there might be interest.

A cursory look at the paper you linked suggests that the main difference
is in labeling and segregating "rotable" dihedral degrees of freedom
from the others. This distinction strikes me as a bit ad hoc and would
likely have to be made in the code specifically for certain molecule
types (e.g. proteins). At present, only improper and standard dihedral
terms are accumulated separately, so this might require semi-elaborate
changes to the code (probably a separate accumulator for the "rotable
dihedral energy and force").

If you want to try doing this yourself, look around the source code for


On 11/29/2015 03:53 AM, Vlad Cojocaru wrote:
> Dear NAMD users/developers,
> I am wondering whether there are plans to implement the new aMD scheme
> developed by Don Hammelberg and co-workers in NAMD ?
> Thanks for answering
> Best wishes
> Vlad
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]
> --
> Brian Radak
> Theta Early Science Program Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
> 9700 South Cass Avenue
> Building 240, 1.D.16
> Lemont, IL 60439-4871
> Tel: 630/252-8643
> email:

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