Hey I have been trying to convert S100A8A9(has two chains) to .gro but after energy minimization I am not getting an integer for the total charge of the system.
Secondly when I try to do molecular dynamics simulation using these parameters: ; 0.5 ps NVT production with Langevin thermostat and GB implicit solvent #################################### INPUT #################################### ld_seed = -1 ; Use random seed ################################# INTEGRATOR ################################## define = -DPOSRES integrator = sd ; Langevin thermostat dt = 0.002 ; Timestep (ps) nsteps = 250 ; Simulation duration (timesteps) nstcomm = 250 ; Center of mass motion removal interval comm_mode = angular ; Center of mass motion removal mode ################################## ENSEMBLE ################################### ref_t = 300 ; System temperature (K) tau_t = 2.0 ; Thermostat time constant (ps) tc_grps = system ; Apply thermostat to complete system ############################## IMPLICIT SOLVENT ############################### implicit_solvent = GBSA ; Generalized Born implicit solvent gb_algorithm = HCT ; Hawkins-Cramer-Truhlar radii calculation nstgbradii = 1 rgbradii = 0.0 ; Cutoff for Born radii calculation (A) gb_epsilon_solvent = 80 gb_saltconc = 0 sa_algorithm = Ace-approximation sa_surface_tension = 2.25936 ########################### NONBONDED INTERACTIONS ############################ cutoff_scheme = group ; Method of managing neighbor lists pbc = no ; Periodic boundary conditions disabled coulombtype = cut-off ; Calculate coulomb interactions using cutoff rcoulomb = 0.0 ; Coulomb cutoff of infinity vdw_type = cut-off ; Calculate van der Waals interactions using cutoff rvdw = 0.0 ; Van der Waals cutoff of infinity rlist = 0.0 ; Neighbor list cutoff nstlist = 0 ; Do not update neighbor list ################################### OUTPUT #################################### nstlog = 50 ; Log output interval (timesteps) nstenergy = 50 ; Energy output interval (timesteps) nstcalcenergy = 50 ; Energy calculation interval (timesteps) nstxout = 50 ; Trajectory output interval (timesteps) nstvout = 50 ; Velocity outout interval (timesteps) nstfout = 50 ; Force output interval (timesteps) I get segmentation fault(11). I don't know what this means. Can you please help me out? -- 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.