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

From: Abir Ganguly (
Date: Tue Jul 09 2013 - 17:35:31 CDT

Hi Giacomo and Aron,

Thanks for the suggestions.

I am using the alchemical simulations implemented in NAMD to calculate
the free energy difference for a particular transformation. However, due
to hysteresis related issues, I need to perform this transformation in
steps. One of the steps is to calculate the loss of configurational
entropy associated with the process of putting these restraints on all
the atoms. The next step would be to calculate the free energy change
for a process within this restrained system.

Hence, the reason for using the colvars (and not constraints) is because
we would like to obtain the free energy of the process as we slowly
remove the restraints.

We will still be doing dynamics because we are restraining the atoms,
and not constraining ( or freezing) them.

In other words, the goal is to restrict the ribozyme to only local
motions, and find out the cost related to that in terms of free energy.

I hope I am not too confusing.



On 07/09/2013 05:16 PM, Giacomo Fiorin wrote:
> 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?
> Giacomo
> 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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