[gmx-users] Usage of position restraint during FEP calculation

[Justin Lemkul]

On 6/6/17 3:45 PM, Геннадий Макаров wrote:
> Dear GROMACS users, I want to estimate binding free energy for small ligand using procedure from article doi:10.1021/jp0217839 that imlies application of one distance, two angle and three dihedral restraints to ligand relatively to receptor. These restraints are controlled by option
> 
> restraint-lambdas
> 
> in *.mdp file, which value varies from 0.0 in source, unrestrained state, to 1.0 in target,  restrained state. But does this value affect position restraints? I need them to restraint part of my receptor. And, if value of restraint-lambdas affects position restraints, how can I exclude this affect? Shall I use six force constants for every position restraint statement in my FEP topology instead of three in usual one?
> 
> 

Quoting the manual for restraint-lambdas:

http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#free-energy-calculations

"Only the restraint interactions: dihedral restraints, and the pull code 
restraints are controlled with this component of the lambda vector."

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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