**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Fri Jul 28 2017 - 19:10:59 CDT

**Next message:**Victoria Lim: "Re: How to calculate free energy to unbias colvars restraint?"**Previous message:**Victoria Lim: "How to calculate free energy to unbias colvars restraint?"**In reply to:**Victoria Lim: "How to calculate free energy to unbias colvars restraint?"**Next in thread:**Victoria Lim: "Re: How to calculate free energy to unbias colvars restraint?"**Reply:**Victoria Lim: "Re: How to calculate free energy to unbias colvars restraint?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

**Next message:**Victoria Lim: "Re: How to calculate free energy to unbias colvars restraint?"**Previous message:**Victoria Lim: "How to calculate free energy to unbias colvars restraint?"**In reply to:**Victoria Lim: "How to calculate free energy to unbias colvars restraint?"**Next in thread:**Victoria Lim: "Re: How to calculate free energy to unbias colvars restraint?"**Reply:**Victoria Lim: "Re: How to calculate free energy to unbias colvars restraint?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Mon Dec 31 2018 - 23:20:28 CST
*