Thanks a lot Justin. On Aug 11, 2014 10:36 PM, "Meenakshi Rajput" <ashi.rajpu...@gmail.com> wrote:
> thanks...can you help me out with the mdp file settings with charmm force > field(proteins)? I am a new user to gromacs and stuck here. > > > On Mon, Aug 11, 2014 at 5:07 AM, Meenakshi Rajput <ashi.rajpu...@gmail.com > > wrote: > >> Thanks..but if potential becomes positive after energy minimisation run, >> then is it normal or there is some prblm with my mdp file. I used the same >> mdp file for this run also. I used charmm force field. >> On Aug 11, 2014 2:32 PM, "Meenakshi Rajput" <ashi.rajpu...@gmail.com> >> wrote: >> >>> 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.