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

From: Giacomo Fiorin (
Date: Tue Jul 09 2013 - 17:16:19 CDT

Hello Abir, you can use the colvars module to restrain the center of mass
of your protein to stay near the dummy, so that the protein doesn't drift
while its internal dynamics is unaffected. This may be helpful for you to
visualize the trajectory, but the FEP calculation doesn't require it.

If you want to restrain each atom individually, that requires defining a
variable for each atom, which in the end defeats the purpose of defining
"collective" variables?

The most efficient way to apply restraints atom-by-atom is still the
"constraints" keyword: what is the reason why you can't use it?


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

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