On 8/2/17 3:23 PM, gangotri dey wrote:
Hello! I am trying to minimize a periodic MnO2 surface using UFF force fields. I have previously computed many structures using MnO2 clusters. I did not face much problem. However, when I am trying to compute the minimization using the following minim.mdp there is segmentation error as follows. ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 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 = 50 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) Error: Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= 3.46301e+34 Fmax= 2.91045e+06, atom= 289 [fen2.hpcc.rutgers.edu:mpi_rank_0][error_sighandler] Caught error: Segmentation fault (signal 11) ./script: line 5: 54036 Segmentation fault (core dumped) gmx_mpi mdrun -ntomp 1 -v -deffnm em I do not understand this problem. Is there anything wrong with my structure or the minim.mdp?
It's either the coordinates or the force field parameters. You have a configuration with an energy on the order of 10^34 kJ/mol, which is essentially infinite, so something is fundamentally flawed.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.