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. 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. -- 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
