Re: How to calculate free energy to unbias colvars restraint?

From: Giacomo Fiorin (
Date: Fri Jul 28 2017 - 19:10:59 CDT

You could try free-energy perturbation, but the two states (restraint on /
restraint off) are probably quite different and convergence may be poor.
An option could be switching the force constant gradually:
(Note the comment in the description.)

>From the technical point of view, you can always re-run the unbiased
trajectory through NAMD to evaluate the energy of Colvars or any additional
energy terms that weren't included originally.


On Fri, Jul 28, 2017 at 7:56 PM, Victoria Lim <> wrote:

> Dear NAMD users,
> I have a molecular dynamics simulation employing a harmonic distance
> restraint using the colvars module in NAMD. I am looking for a way to
> calculate the free energy of removing the restraint so that I can correct
> data from the calculations using the restraint. Is there a way I can
> re-evaluate the energies of a stored trajectory with the restraints turned
> off?
> Thank you!
> Ria

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:30 CST