Hi Valentina -
Honestly, I did not get the considerations with charges. TI probably
scales interaction energies between selected groups, not charges.
Science-wise, I would first decouple organic particle, then decouple
chloride anions, and place a right sign between these two free
energies. If you substitute an ion in the neutral system by a
molecule, your system free energy will not definitely like this giving
a positive (delta)G.
Dr. Vitaly V. Chaban
On Fri, Mar 14, 2014 at 4:52 PM, Valentina
valentina.erast...@durham.ac.uk wrote:
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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