[gmx-users] angle/distance/position restraints in alchemical free energy calculation

Wes Barnett w.barnett at columbia.edu
Fri Nov 3 14:37:17 CET 2017

On Fri, Nov 3, 2017 at 2:00 AM, minky son <minky0710 at gmail.com> wrote:

> Dear gmx user,
> I’m studying about alchemical free energy calculation.
> I have been read some articles about restraints during free energy
> calculation, they referred the procedure in the article (
> http://pubs.acs.org/doi/pdf/10.1021/jp0217839).
> I tried to search mailing list, but still I couldn’t understand.

I don't see any indication in that article of the researchers using
GROMACS. It looks like they are using CHARMM.

> The manual said “restraint-lambdas” option only handle dihedral
> restraints, and the pull code restraints
> How to apply angle/distance/position restraints with respect to lambda?

I don't believe those other restraints can be coupled for free energy
changes in GROMACS at this time.

James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu

More information about the gromacs.org_gmx-users mailing list