Thanks. This helps. One more question, is it possible to further break down the energy interactions between a piece of a protein and another piece of the solvent? For example, if I wanted the Cou and vdw interactions specifically for an -OH group on a solvent and some chain on the solute. I know how to do this using make_ndx for g(r) plots but I don't see how you can apply it to energygrps on the *.mdp file.
Thanks again for all your help. -Fabian On Thu, Feb 23, 2012 at 2:41 PM, Fabian Casteblanco <[email protected]> wrote: > Thanks. So before I run the simulation, I must use energygrps (for > example: energygrps: Protein SOL) in my md.mdp file so that it knows > to write down specific interactions between the two groups. Will > then it simply appear when I later run g_energy? > > -Fabian > > > --------------------------------------------------------------------------------------------------------------------------------------------------------- > Short-range nonbonded interactions can be decomposed using proper energygrps > in > the .mdp file. > > Perhaps, but g_enemat also requires that energygrps are specified when running > the simulation. Otherwise, the applicable terms in the .edr file are not > decomposed. > > -Justin > > > > On Thu, Feb 23, 2012 at 1:56 PM, Fabian Casteblanco > <[email protected]> wrote: >> Hello everyone, >> >> Is it possible to see the energy (LJ, Cou) for simply the solute >> interacting with the solvent? >> >> For example, g_energy will calculate all the energies for the entire >> system interactions which include solvent-solvent interactions. I >> would simply like the solute-solvent interactions or possibly simply >> the solvent-solvent interaction energies. I see g_enemat as a >> possible function to use. Is this the best way? >> >> Thanks. >> >> -- >> Best regards, >> >> Fabian F. Casteblanco >> Rutgers University -- >> Chemical Engineering > > > > -- > Best regards, > > Fabian F. Casteblanco > Rutgers University -- > Chemical Engineering -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
