Jinyao Wang wrote: >> Jinyao Wang wrote: >>> Hi gmx-usersé”›? >>> >>> I want to calculate the non-bond interaction (LJ+Coulomb) between solvent >>> and >>> solvent in pure solvent system. After the simulation of my pure solvent >>> system, I calculated the interaction between solvent and solvent using the >>> rerun option of the "mdrun program". First, I set the energygrps = sol sol >>> in rerun.mdp file. Then, I make the grompp program like this, grompp -f >>> rerun.mdp -c conf.gro -n index.ndx -p pure.top -o rerun.tpr But this step >>> has >>> a fatal error: Atom 1 in multiple energy Mon. groups (1 and 2) >>> >>> I don't know how to solve the problem and I want to know whether this method >>> is effective for calculating the interaction between solvent and solvent in >>> pure solvent system. >>> >>> Any suggestion will be appreciated. >>> >> These terms should already be present in the .edr file. Run g_energy and >> have a >> look. >> >> -Justin > > > 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.
Since you only have solvent in your system, the entire non-bonded contribution is from solvent-solvent interactions. That's already reported in g_energy. If you're trying to ask about calculating something else, please rephrase your question. 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
