[gmx-users] Water molecule can not be settled

[Amali Guruge]

Dear Gromacs users,

My system contains water molecules and polyethylene glycol molecules. I
generated the box (15.2*15.2*15.2 nm*3) using genbox command. Thereafter,
PEG molecules were added using gmx insert-molecules and solvated with gmx
solvate.

When I tried to run md, I got the following error.

step 1802: Water molecule starting at atom 93528 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)

my rum.mdp file contains following parameters.

integrator    =  md
dt        =  0.005
nsteps        =  1000000
comm_mode    =  linear
;
nstxout        =  500000
nstlog        =  1000
nstenergy    =  50
nstxtcout    =  10000
;
cutoff-scheme   =  Verlet
nstlist         =  10
ns_type         =  grid
pbc             =  xyz
rlist           =  1.4
;
coulombtype     =  PME
rcoulomb        =  1.4
epsilon_r       =  1
rvdw            =  1.4
fourierspacing  =  0.12
pme_order       =  4
ewald_rtol      =  1e-5
DispCorr        =  EnerPres
;
Tcoupl        =  v-rescale
tc-grps        =  System
tau_t        =  .1
ref_t        =  298
;
Pcoupl        =  parrinello-rahman
Pcoupltype    =  isotropic
tau_p        =  2.0
compressibility    =  4.5e-5
ref_p        =  1.0
;
gen_vel        =  no
;
constraints    =  all-bonds
constraint_algorithm    =  lincs
lincs_order    =  8


Can anyone help me to solve the error. The most of the people commented
previously that this error is due to a bad starting structure. If it is the
reason, how can I correct it.

Thank you.

Sincerely,
A Guruge