[gmx-users] Re: simulation crash with GROMOS96 force field

[Vitaly V. Chaban]

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?
>