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.
