[gmx-users] binding free energy calculations on charged ligands

Diane Fournier diane.fournier at crchul.ulaval.ca
Fri Sep 15 16:45:50 CEST 2006

Hello all,
I'm still trying to get the binding free energy for my ligands, and I now think I will have to do another simulation, since my first one used PME and I didn't record velocities in my trajectory.
But first I need some advice, since I can't find a paper which describes unambiguously what I want to do. 
First, my ligand is charged (carboxylate) ; what is the best (and easiest) method to calculate the binding free energy for charged ligands ? Is MM-PBSA preferable to LIE in that case ?
I tried LIE with PME, and I know that you can get the PME contribution by doing a mdrun -rerun with zero charge on all charge groups alternatively. I also understand that this was described in the mail archive, but I can't find the mails in question. Can somebody tell me exactly when those mails were written ?
And do the 'standard' settings for PME (as described in the manual) need to be changed ? I understand that the Coul-LR and LJ-LR terms are not produced when rcoulomb = rlist and rvdw = rlist respectively ? Or those are the terms that are calculated in the zero-charged reruns ?
Also, what is to be done with the counterions ? Since it does not seem possible to have an equilibrium distribution in a reasonable time (on a ns scale), must I run the simulations without them ? 
All advice will be very appreciated.
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