Re: Accelerated Molecular Dynamics

From: Vijay Vammi (
Date: Wed Nov 02 2011 - 20:42:07 CDT

Hi all,

I am performing acclerated MD simulations and want to protect omega
dihedrals from getting distorted. Instead of adding additional restraints
input, i thought it might be a good solution to increase the force constant
of the omega dihedral angle.

I use amber forcefields and I am not able to figure out how the system
works. I was able to figure that all my omega dihedrals would be CT-C-N-CT,
so is it sufficient to update

X -C -N -X 4 10.00 180.0 2. AA,NMA in
parameter file to take a high value. (there are no cis-peptides in this
particular protein).

 For the charmm forcefields, I have identified all the types of dihedral
that could happen (CT1-C-NH1-CT1 and varities). Is there a easier way to
update them all using a wildcard or so.

Please advice.

On Tue, Oct 25, 2011 at 9:04 PM, Vijay Vammi <> wrote:
>> 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.
>> Thanks
>> Santhosh
>> 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
>>> 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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