[gmx-users] Check for bad contacts and/or reduce the timestep

[Md. Imrul Reza Shishir]

Dear all
I have simulated my system 7 different temperature from 300K~500K.Every
time I simulated for 10ns. But when I run the simulation above 500K (I.e
530K/550K/560K) the simulation was crash in NPT equilibrium stage with
following warning.

*step XXX: Water molecule starting at atom XXXX can not be settled. Check
for bad contacts and/or reduce the timestep if appropriate.*

​What should be cause for that?

my energy minimization  ​stage:
*minim.mdp*
title            = OPLS Cellulose EM_steep simulation
integrator        = steep
emtol            = 1000.0     kJ/mol/nm
emstep              = 0.0001
nsteps            = 50000
nstlist            = 10
cutoff-scheme            = verlet
ns-type                = grid
coulombtype            = PME
pme-order            = 4
fourierspacing        = 0.12
rlist                  = 1.2
rlistlong            = 1.4
rcoulomb            = 1.2
rvdw                = 1.2
pbc                = xyz
periodic-molecules      = yes
constraints            = none
vdwtype               = Cut-off

my npt equilibrium:
*npt.mdp*

title            = Cellulose OPLS-AA NPT equilibration
define            = -DPOSRE
integrator        = md
nsteps            = 250000
dt            = 0.002
comm-mode        = Linear
comm-grps               = System
nstcomm            = 100
pbc            = xyz
nstxout            = 500
nstvout            = 500
nstenergy        = 500
nstlog            = 500
nstxout-compressed      = 500
compressed-x-grps       = System
cutoff-scheme       = verlet
ns-type                = grid
nstlist                = 10
rlist                  = 1.2
rlistlong            = 1.4
coulombtype            = PME
pme-order            = 4
rcoulomb            = 1.2
vdwtype               = Cut-off
rvdw                = 1.2
fourierspacing        = 0.12
DispCorr        = EnerPres
continuation        = yes
constraint-algorithm    = lincs
constraints            = all-bonds    ;
lincs-iter            = 1
lincs-order            = 4
tcoupl            = v-rescale
tc-grps            = Other    Water    Ion
tau_t            = 0.1    0.1    0.1
ref_t            = 550     550    550
pcoupl                = Parrinello-Rahman
pcoupltype            = isotropic
tau-p                = 1.0
ref-p                = 1.0
compressibility         = 4.5e-5
refcoord_scaling        = com        ;

; Velocity generation
gen-vel            = no


​Thank you in advance. ​

-- 
*Md Imrul Reza Shishir*
Master Student
​