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

Justin Lemkul jalemkul at vt.edu
Fri Nov 3 14:39:38 CET 2017

On 11/3/17 9:36 AM, Wes Barnett wrote:
> 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.

And to make it really simple:


The protocol is described in full in 


>> 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.


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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