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.
Diane
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