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

[nishap.patel at utoronto.ca]

Hi,

  I am trying to run a simulation with 1360 Tip4p water molecules and  
one methane molecule (Box size: 35.500 35.3371 35.500 and Total 5541  
atoms) but I am getting the error:

t = 0.000 ps: Water molecule starting at atom 5433 can not be settled.
Check for bad contacts and/or reduce the timestep.

Here is my grompp. file :


; RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0.0
dt                       = 0.002
nsteps                   = 25000
; number of steps for center of mass motion removal =
nstcomm                  = 1

  ENERGY MINIMIZATION OPTIONS
emtol                    = 10000
emstep                   = 0.01

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 1000
nstvout                  = 1000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 0
nstenergy                = 100
; Output frequency and precision for xtc file =
nstxtcout                = 100
xtc_precision            = 1000
; This selects the subset of atoms for the xtc file. =
; Only the first group gets written out, it does not make sense =
; to have multiple groups. By default all atoms will be written =
xtc_grps                 =
; Selection of energy groups =
energygrps               = CH4 SOL


; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 1.0
; ns algorithm (simple or grid) =
ns_type                  = grid
; nblist cut-off         =
rlist                    = 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulomb_type             = pme
rcoulomb_switch          = 0
rcoulomb                 = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 1.0
epsilon_rf               = 0
; Method for doing Van der Waals =
vdw_type                 = Cut-off
; cut-off lengths        =
rvdw_switch              = 0
rvdw                     = 1.0
dispcorr                 = enerpres

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl                   = v-rescale
; Groups to couple separately =
tc-grps                  = system
; Time constant (ps) and reference temperature (K) =
tau_t                    = 0.1
ref_t                    = 300

; Pressure coupling      =
Pcoupl                   = Berendsen
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 1.0
compressibility          = 4.6e-5
ref_p                    = 1


; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 171533

I am new to this, so any inputs would be appreciated.

Thanks

Nisha