[gmx-users] Re: simulation crash with GROMOS96 force field
Vitaly V. Chaban
vvchaban at gmail.com
Mon Jan 25 21:30:15 CET 2010
Please find below
===============================
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 1000000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode =
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
;bd-temp = 300
;bd-fric = 0
;ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 50
emstep = 0.005
; Max number of iterations in relax_shells
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 5000
nstenergy = 2500
; Output frequency and precisiofor xtc file
nstxtcout = 50
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 50
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.45
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Reaction-Field-zero
epsilon_rf = 0
rcoulomb-switch = 0
rcoulomb = 1.3
vdw-type = Shift
; cut-off lengths
rvdw-switch = 1.1
rvdw = 1.3
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; 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 = 348
; Pressure coupling
Pcoupl = no ;Parrinello-Rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-6
ref_p = 1.00
; Random seed for Andersen thermostat
andersen_seed = 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen_temp = 298.15
gen_seed = 1993
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are exclud
energygrp_excl =
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) to energy file
nstorireout = 100
; Dihedral angle restraints: No, Simple or Ensemble
dihre = No
dihre-fc = 1000
; Output frequency for dihedral values to energy file
===============================
On Mon, Jan 25, 2010 at 10:27 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Vitaly V. Chaban wrote:
>>>
>>> 1. No problem at all in vacuo? That with a 1 fs timestep and the sd
>>> integrator? Strange then that your molecule is ok and the water is ok,
>>> but they are unstable together. Perhaps your'e not getting any LJ
>>> interactions (or not correct ones) between your solute and water? That's
>>> where I would focus my efforts if I was you. I suppose it could also be
>>> solute-solute LJ problems...
>>
>> If I switch off electrostatics between CIP and water, the problem
>> disappeared... Maybe it's really worth to use a smaller timestep for
>> this system ...
>
> Can you post your .mdp file?
>
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