Hi, In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the lipids, I need to follow the iteration while the cutoff value changed to 0. I' d like to know what settings of EM.mdp file are suggested to get the best results of doing shrinking steps? When I set the settings as follow, the lipids interfere the peptide however the APL doesn't get the experimental value. So the configuration is not ideal to get through the equilibrium steps.
define = -DPOSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force < 100.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 0.4 ; Cut-off for making neighbor list (short range forces) rlistlong = 6.0 coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 0.4 ; Short-range electrostatic cut-off rvdw = 0.4 ; Short-range Van der Waals cut-off vdwtype = switch rvdw_switch = 0.2 pbc = xyz ; Periodic Boundary Conditions Now, I am wondering if such a settings will serve a proper deletion radius? Sincerely, Shima -- 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
