[gmx-users] FEP with position restraints

David Fernández Payeras david.fernandez at uib.es
Wed Mar 30 14:04:28 CEST 2016

Dear all, 
I'm trying to calculat the binding free energy for a ligand-protein system. I
tried to calculate it without restraints but the ligand moved away from the
active site. Thus, now I'm trying it by using position restraints for three ions
of the active site and three atoms of the ligand. I'm using the FEP method in
two decoupling steps (Coulomb and then vdW interactions). However, when I
executed the g_bar command the program reported this warning.

WARNING: Some of these results violate the Second Law of Thermodynamics:
This is can be the result of severe undersampling, or (more likely)
there is something wrong with the simulations.

Actually, I don't know if it's is normal because i'm using position restraint,
and if it is so, how can I solve it?  

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