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

Justin Lemkul jalemkul at vt.edu
Mon Nov 6 02:39:03 CET 2017

On 11/5/17 8:35 PM, minky son wrote:
> I want to do it using gromacs.
> Is there any way to control those restraints (except dihedral angle) in
> gromacs?

You can set up any sort of bonded interactions (all of which can be 
perturbed via the free energy code) using an 
[intermolecular_interactions] directive at the end of the .top file. You 
can specify pretty much any kind of interaction (bond, angle, dihedral, 
etc) using global atom numbers. They aren't restraints, but normal 
bonded interactions, hence why you can perturb them.



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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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