[gmx-users] Check for bad contacts and/or reduce the timestep.
shivangi.nangia at gmail.com
Tue Mar 29 20:01:59 CEST 2011
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
I am trying to to do a NVT equilibration which runs into the following
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
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)
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
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?
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