From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
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:
http://colvars.github.io/colvars-refman-namd/colvars-
refman-namd.html#x1-770006.4.3
(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.
Giacomo
On Fri, Jul 28, 2017 at 7:56 PM, Victoria Lim <limvt_at_uci.edu> 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 http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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