Thank you I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. Could you explain how can I observe bad contacts in the structure? I even tried the different box size but it didn't work. Both ligand and protein are ok with minimization separately.
> On Apr 19, 2020, at 11:13 PM, Elham Taghikhani <elham802...@yahoo.com> wrote: > > > Hi > > I am simulating a protein-ligand system, using oplss force field but i got > this error during minimization. > > Steepest Descents: > Tolerance (Fmax) = 1.00000e+03 > Number of steps = 50000 > Step= 0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 > Segmentation fault (core dumped) > > and this is my mpd file: > ; LINES STARTING WITH ';' ARE COMMENTS > title = Minimization ; Title of run > > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < > 10.0 kJ/mol > 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 > cutoff-scheme = Verlet > 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 > vdwtype = cutoff > vdw-modifier = force-switch > rvdw-switch = 1.0 > rvdw = 1.2 ; long range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions > DispCorr = no > Can anyone suggest how to troubleshoot this error? > The system is nuetralized. > > Thank you in advance. > -- 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.
