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

From: Abir Ganguly (
Date: Tue Jul 09 2013 - 17:01:15 CDT

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.



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