Re: Accelerated Molecular Dynamics

From: Yi Wang (
Date: Tue Oct 25 2011 - 18:03:33 CDT

Hi Santhosh,

        Currently the aMD implementation in NAMD can't let you selectively apply the boost to certain dihedrals, and from the implementation side, it's actually quite tricky how to do this effectively---we did give it some thought but didn't proceed due to the substantial amount of time the coding might require.

        An alternative at this point is perhaps to add some restraints to protect those omega dihedrals being distorted by the boost?


On Oct 25, 2011, at 2:11 PM, Vijay Vammi wrote:

> Hi,
> 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.
> Thanks
> Santhosh

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