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

[Геннадий Макаров]

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?


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Геннадий Макаров