Re: harmonic-restraints/colvars

From: Jérôme Hénin (
Date: Tue Jan 14 2020 - 04:25:06 CST

Hi Francesco,

That is allowed at a technical level: NAMD's harmonic restraints and
Colvars will work side by side - I suppose you know that, but I am
repeating it for the benefit of others who'd read this thread based on its
subject line.

I cannot tell you what is scientifically relevant for your specific system:
any set of restraints is legitimate, but then the simulations explore a
different ensemble, and that of course limits the information that can be
gained from them. Possibly to the point where everything significant is
restrained, and the simulation becomes completely uninformative.


On Tue, 14 Jan 2020 at 10:49, Francesco Pietra <>

> Hello: is that allowed using a mixture (for different groups of atoms) of
> harmonic restraints (by creating a pdb file marked with different values on
> column B) and distance colvars?
> Could that be equivalent to, or be more appropriate than by, using a
> mixture of distance and rmsd colvars for the same different groups of atoms?
> The question is related to getting a MD stable system by keeping an
> organic ligand at its binding pocket in a model that results from cutting
> the natural huge biomolecule all around the ligand.
> So far (despite parameterization of the ligand at the state of the art
> with CGenFF, whereby it proved stable in TIP3P for hundreds of ns) I was
> unable to get a stable system when removing all restraints/colvars except
> at the region where the biopolymer was cut..
> thanks for a general advice
> francesco pietra

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