Re: Accelerated Molecular Dynamics

From: Vijay Vammi (
Date: Tue Oct 25 2011 - 21:04:49 CDT

Hi Yi,

Thanks for the reply. I like the idea of adding additional restraints to
the omega dihedrals.

Since I am interested in protecting all the omega diherdals, is it wise to
increase the Kdihedral(may be double or triple the original value) in the
parameter file for the atom types?
I am right now doing a manual changie of the K for different combinations
that I observe from the psf file for the omega angle.

Is there a better way ? I did notice cispeptide plugin in VMD which gives a
restraint file but I thought this might be a good solution.


On Tue, Oct 25, 2011 at 6:03 PM, Yi Wang <> wrote:

> 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?
> Best,
> Yi
> 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
> >
> > 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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