Re: restraining bonds

From: Kenno Vanommeslaeghe (
Date: Tue Sep 02 2014 - 11:04:37 CDT

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Harmonic *RE*straints will do little to suppress the vibrational DOF
associated with the bonds; it will just shift them to higher frequencies,
and if you shift them very far up (which could arguably have a similar
effect as suppressing them), then the integrator gets in trouble. To me,
it looks like you want *CON*straints for this job. This is supported
through the rigidBonds facility, though it is not clear to me whether NAMD
allows defining rigidBonds between heavy atoms, and if yes, how.
All I know is that both GROMACS and CHARMM allows doing this, and that
some force fields (not CHARMM) require it.

On 09/01/2014 11:33 PM, Neelanjana Sengupta wrote:
> We are interested in understanding the effects of the vibrational D.O.F of
> a protein on certain properties, and hence are trying to suppress those to
> whatever extent possible..
> On Mon, Sep 1, 2014 at 9:07 PM, Kenno Vanommeslaeghe
> < <>> wrote:
> *From:*Neelanjana Sengupta [
> <>]
> *Sent:* Monday, 1 September 2014 4:04 PM
> *To:* Tristan Croll
> *Subject:* Re: namd-l: restraining bonds
> No, I am not seeking to restrain a group of atoms w.r.t a reference
> structure, but rather to restrain the vibrations of the large
> number of
> bonds in my protein. Thanks for the suggestion, though..
> Excuse me my curiosity, but why on earth would you want to do that?
> Covalent bonds are *already* defined by a harmonic potential, so all
> you can accomplish by adding harmonic restraints on top is to
> artificially increase their harmonic frequencies, which may
> destabilize the integrator if the restraints are strong enough.
> It does seem plausible there might exist good reasons to *CON*strain
> the bonds (though I can't think of them right now), but that would be
> accomplished differently.

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