From: Victoria Lim (limvt_at_uci.edu)
Date: Fri Jul 28 2017 - 19:17:33 CDT
Giacomo, when you say to re-run the unbiased trajectory through NAMD, does
that mean an additional simulation? Can you expand further on how to do
On Fri, Jul 28, 2017 at 5:10 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> 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:
>> 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
>> Thank you!
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
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