Re: restraining bonds

From: Kenno Vanommeslaeghe (
Date: Mon Sep 01 2014 - 10:37:17 CDT

> *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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