[gmx-users] Regarding pdb2gmx and mdrun

[S M Bargeen Turzo]

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?