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 > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Free-energy-calculation-of-a-charged-system-tp5015154.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.