[gmx-users] free energy calculation and g_bar error

Chunxia Gao chunxia.gao at chem.gu.se
Tue Apr 24 11:52:27 CEST 2012

Dear gmx-users:

I was trying to do a free energy calculation of a charged ligand, according to the paper "Calculation of  Absolute Binding Free Energies for Charged Ligands and Effects of  Long-Range Electrostatic Interactions ", one of the problems with charged ligands is that the use of a solvent-solvent cutoff causes an overpolarization of the the solvent toward the solute charge, but this can be done by not using any cutoffs at all (If I did not misunderstand it).

In the following, this is my part of mdp parameter for non-charged ligand:

; Neighborsearching and short-range nonbonded interactions
nstlist                     = 10
ns_type                   = grid
pbc                         = xyz
rlist                         = 1.2
; Electrostatics
coulombtype            = PME
rcoulomb                 = 1.2
; van der Waals
vdw-type                 = switch
rvdw-switch             = 0.8
rvdw                       = 0.9

for charged ligand, it is like this:

; Neighborsearching and short-range nonbonded interactions
nstlist                  = 0
ns_type                  = simple
pbc                      = no
rlist                    = 0.0
; Electrostatics
coulombtype              = cut-off
rcoulomb                 = 0.0
; van der Waals
vdw-type                 = cut-off
rvdw-switch              = 0.0
rvdw                     = 0.0

Is this correct for what it means in the paper that by using no cutoff at all?

Anyway, I presume that this is correct, and run some free energy calculation, when I used the g_bar to calculate the results, I got the error message like this :

Fatal error:
Some dhdl files contain only one value (dH/dl), while others
contain multiple values (dH/dl and/or Delta H), will not proceed
because of possible inconsistencies.

So what does it mean?

Thank you for answering my questions in advance.


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