hi users i have run energy minimisation of docked complex by using this min.mdp:-
cpp = /lib/cpp ; Preprocessor include = -I../top ; Directories to include in the topology format integrator = steep emtol = 1000 ; Stop minimization when the energy changes by less than emtol kJ/mol. nsteps = 200 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps = Protein ; Which coordinate group(s) to write to disk energygrps = Protein ; Which energy group(s) to write to disk nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; long range electrostatic cut-off rvdw = 1.2 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no0 After the run, potential energy is negative. can you tell me whats the problem?? -- 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.