[gmx-users] check for bad contacts and/or reduce the time step if appropriate

[Daniele Veclani]

Dear Gromacs Users,

I am trying to simulate a box with 1000 waters.  The box size are of
31,07625 A per side. When I go to do the dynamic simulation (mdrun -s
1000w.tpr -c 1000w_1.gro, I use force field opls-aa) comes out this error
message:

step: XX: Water molecule starting at atom xxx can not be settled
check for bad contacts and/or reduce the time step if appropriate
Wrote pdb files with previous and current coordinates

my .mdp file is:

; 7.3.3 Run Control
integrator                  = steep
nsteps                      = 50000
; 7.3.5 Energy Minimization
emtol                         = 1000
emstep                      = 0.001
; 7.3.8 Output Control
nstxout                        = 100
nstvout                        = 100
nstfout                         = 100
nstlog                           = 1
nstenergy                     = 1
energygrps                   = System
; 7.3.9 Neighbor Searching
cutoff-scheme               = Verlet
verlet-buffer-tolerance   = 0.005
nstlist                             = 10
ns_type                         = grid
pbc                                = xyz
rlist                                 = 1.2
; 7.3.10 Electrostatics
coulombtype                 = PME
rcoulomb                       = 1.2
; 7.3.11 VdW
vdwtype                        = cut-off
rvdw                              = 1.2
DispCorr                       = Ener
; 7.3.13 Ewald
fourierspacing               = 0.12
pme_order                    = 4
ewald_rtol                      = 1e-5

can anyone please let me know what is wrong with my system

Best regards
Daniele Veclani