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

Dr. Vitaly Chaban vvchaban at gmail.com
Fri Mar 14 18:32:33 CET 2014

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.erastova at 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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