On Mon, Sep 23, 2013 at 2:40 PM, Jong Wha Lee <jongwh...@postech.ac.kr> wrote: > 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
