Dear Vitaly,
Thank you very much for your reply. I originally asked the question because I wasn't sure my values were from correct procedures. Now I see how I could properly calculate binding energies with MM. John Lee > Dear Vitaly, > > > > Thank you for your suggestion. > > > > I have also tried calculating interaction energies by specifying > energygrps in .mdp file, but calculated energies deviate greatly from > QM calculated energies and experimental results. I suspect that the > structure of each component in complex differs from the structures > when they were alone, because this will lead to a deviation in > equilibrium binding enthalpy from the interaction energies that is > calculated with energygrps line in .mdp file. This might be because of electrostatics treatment method. Use simple cut-off scheme and specify a really large cut-off radius, which exceeds the sum of the sizes of your binding particles. I made tons of such comparisons, QM vs. MM. It works pretty well. > > My guest of interest have two charges at a short distance, which is > very unfavorable and the charges will try to be furthest apart. > However, my host molecule can stability the charges via oppositely > charged groups, and so now the guest molecule forms a bent structure. > In this case, shouldn't the change in energy due to the different > conformation of the guest be taken into account, to discuss > equilibrium binding enthalpy? I feel maybe this wouldn't be well represented with interaction energies. The binding energy is an energy gain, dE, in the following reaction A + B -> AB, dE A, B, and AB are optimized geometries: in vacuum, in solvent or anywhere. So, if a molecule changes its conformation during binding, this energy gain/loss should be a part of the binding energy, I see no methodological problem here. Dr. Vitaly V. Chaban -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
