Accelerated Molecular Dynamics

From: Vijay Vammi (
Date: Tue Oct 25 2011 - 16:11:54 CDT


I have been using NAMD's implementation of Accelerated Molecular dynamics
for my research. Thanks for the implementation of the feature in NAMD.

In the original paper of AMD, there was no discrimination between the
different torsional angles (phi, psi, omega or chis). And the boost was
provided to all the dihedrals when required.
While running AMD simulations I have observed that the Omega torsional
angle does get distorted (standard geometry being near 180) to values close
to 140 sometimes which is highly strained omega.

Would there be any functional difference if dihedral potential concerning
Omega was not boosted or scaled to a value lower than phi/psi/chi boost? Is
it possible to implement such a feature into NAMD(local for testing)
without affecting the performance? Hope I was clear in my question.


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