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

[shivangi nangia]

Hello gmx-users,

I have a 5 ang box with equal number of water and methanol molecules (1800),
a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system is overall
+2 charged.

I am trying to to do a NVT equilibration which runs into the following
error:


t = 0.000 ps: Water molecule starting at atom 11816 can not be settled.
Check for bad contacts and/or reduce the timestep.

the nvt.mdp is:

title    = hist NVT equilibration
define      = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md     ; leap-frog integrator
nsteps      = 50000     ; 2 * 50000 = 100 ps
dt    = 0.002    ; 2 fs
; Output control
nstxout     = 100    ; save coordinates every 0.2 ps
nstvout     = 100    ; save velocities every 0.2 ps
nstenergy   = 100    ; save energies every 0.2 ps
nstlog      = 100    ; update log file every 0.2 ps
; Bond parameters
continuation   = no     ; first dynamics run
constraint_algorithm = lincs  ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1      ; accuracy of LINCS
lincs_order = 4      ; also related to accuracy
; Neighborsearching
ns_type     = grid      ; search neighboring grid cells
nstlist     = 5      ; 10 fs
rlist    = 1.0    ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0    ; short-range electrostatic cutoff (in nm)
rvdw     = 1.0    ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME    ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4      ; cubic interpolation
fourierspacing = 0.16      ; grid spacing for FFT
; Temperature coupling is on
tcoupl      = V-rescale ; modified Berendsen thermostat
tc-grps     = Protein Non-Protein   ; two coupling groups - more accurate
tau_t    = 0.1 0.1   ; time constant, in ps
ref_t    = 250    250   ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl      = no     ; no pressure coupling in NVT
; Periodic boundary conditions
pbc      = xyz    ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = yes    ; assign velocities from Maxwell distribution
gen_temp = 250    ; temperature for Maxwell distribution
gen_seed = -1     ; generate a random seed

I did try to reduce the timestep from 2 fs to 1 fs but ran into the same
error.



Searching through a few archives I got a hint it is something do to with
water's density per cubic nm.
Is that whats going on here?
If yes, then how do I randomly delete some water molecules from my system?

Please help.

Thanks,
Shivangi
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