Re: use of colvars to restrain the absolute positions of all atoms in a large system

From: Aron Broom (
Date: Tue Jul 09 2013 - 17:18:35 CDT

If you are totally restraining all absolute positions, you aren't really
doing dynamics, and you could get you answer faster by just calculating the
energy difference between two snapshots, since entropy wouldn't be a thing
in your system anyway.

But if your just trying to keep the ribozyme held together in a global
sense, but still allow local movements and fluctuations, you might want to
consider, rather than the many harmonic restraints method, using the RMSD
colvar, and simply restraining it to within 2-4 angstroms or something
reasonable for your size of molecule. Then use an orientation or angle
colvar relative to the absolute axis in order to stop the ribozyme from
rotating in space.


On Tue, Jul 9, 2013 at 6:01 PM, Abir Ganguly <>wrote:

> Hi NAMD users,
> I have a very specific question regarding the use of the colvars module
> that I am stating below.
> I am trying to use the colvars module to restrain the absolute positions
> of all the atoms in my system, which is a ribozyme. I am running some
> alchemical FEP simulations on the system and I need to fix(restrain) the
> positions of all these atoms during the simulations.
> I can not use the constraints option in NAMD because of reasons that I can
> state later, if required.
> I realize that I can define a dummy atom, and can use the 'distance'
> option in colvar to harmonically restrain the position of all atoms to that
> dummy atom. I was curious what would be a clean and smart way to go about
> it, since I have so many atoms. It will be really helpful if there are some
> templates with these sort of colvars, so that I can get some directions as
> to how to build my input file.
> Thanks,
> Abir

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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