Hi gromacs user, A peptide(p), a solid surface(s) in water(w) solution are the three ingredients of my system. The total internal energy (Utot) of the system in NVT ensemble, can be defined as Utot = Upp + Uww + Upw + Usw + Ups , where the Uxy is the internal energy of interaction between x and y. Now my question is that how I can simulate each of these portion in a NVT ensemble simulation?
I use the "energygrps = peptide surface water" in my mdp file, but my gmx energy -f case.edr does not contain any of those Uxy, but it has something like Coul(LJ)-SR:x-y, Coul(LJ)-14:x-y, I was wondering if the sum over these Coul(LJ):x-y would give me the Uxy? Also, is the "Total-Energy" in the gmx energy the total internal energy of the system Utot which shows up in the Helmholtz free energy, A = Utot-TS? Thanks, Kind regards, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
