Jinyao Wang wrote: >>> Hi Justin, Thank you for your reply. But I still don't know how to set the >>> "energygrps" option in the rerun.mdp for calculating the interaction between >>> solvent molecule and solvent molecule in pure solvent system. As you said >>> that these terms should be obtained running the g_energy,could you give me >>> some details about the "energygrps" option in rerun.mdp file or how to >>> calculate the intermolecular interaction in pure solvent system. Thanks in >>> advance. >>> >> If you have a pure solvent system, there is no way to set separate >> energygrps, >> as you found out earlier. There is also no need to re-run your simulation. >> Use >> g_energy to analyze your original ener.edr file; you will see the LJ and >> Coulombic terms in the list of options. >> >> -Justin > > Hi Justin, > My simulation system is pure benzaldehyde system. I set the option nrexcl = > 3. > So I think the LJ and Coulombic terms include intermolecular interaction > energy and intremolecular interaction eneryg (e.g. between atom and atom)
When you didn't state what your solvent was, we presumably all assumed it was small enough that there were no intra-molecular interactions, since that's normally the case with solvent molecules in biomolecular MD. Please learn from this - we've all wasted a bunch of time and emails because you didn't make a good enough description of the problem. You're right that those total terms do include intra-molecular contributions. To exclude them, do a rerun with a .tpr based on a .top that uses a sufficiently high nrexcl, or manual [exclusions]. Energy group exclusions exclude sets of interactions between groups, which would work here only if you defined a group for each molecule and a pair between each molecule and itself (and that was legal... dunno about that). Mark _______________________________________________ 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/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/mailing_lists/users.php
