[gmx-users] Free energy calculation of a charged system

[Valentina]

Hello,

I need an advise on how it is better to approach the ThermoD integration of
such system:
+vely charged inorganic layer, filled with water and counterbalanced by -ve
organics

Do I integrate out organics both VdW and Coulomb, making the system have
total +ve charge at lambda = 1

OR:

Do I integrate out organics only by VdW, leaving Couloumb interactions, by
such having a neutral system at lambda = 1

I ideally want to compare the free energies of the substituting Cl- ions
with organic molecules, but I don't think I can just change Cl- at lambda =0
for an organics at lambda =1 (or can I?) Therefore I was planning to perform
Thermod integration of both systems independently, also Cl- and organics in
vacuum (again charges issue) and calculate partition ratios. 

Thank you for advise,
V

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