[gmx-users] mdp file

[He, Yang]

Hi all users,

When I use the command "mdrun -tablep table.xvg " to run my model in gromacs,  it always shows that:

starting mdrun 'DNA in water'
10000 steps,     20.0 ps.

Warning: 1-4 interaction between 11 and 19 at distance 1.437 which is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

And no more information . Furthermore, I use the command ngmx to look at the trajectory , I found that  only when I set the value of nsteps by 10,  will there be little animation about my DNA two strands' disassociation . While I try to reduce the value of dt , nstdisreout , nstorireout and nstdihreout , it also did not work and I can not see any disassociation of DNA strands  using the command "ngmx".

Also, what I got confused is that when I set the value of nsteps larger than 10, there is just static figure about DNA model.  This is my part of mdp file

; Start time and timestep in ps
tinit                    = 0
dt                       = 0.002
nsteps                   = 10000
; For exact run continuation or redoing part of a run
init_step                = 0
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                =




; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 10
; 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                    = 0.686
domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = User
rcoulomb-switch          = 0
rcoulomb                 = 0.9
; Relative dielectric constant for the Cut-off or DC of the reaction field
epsilon-r                = 78
; Method for doing Van der Waals
vdw-type                 = User
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Seperate tables between energy group pairs
energygrp_table          =
; 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

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm             = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii               = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                 = 2
; Salt concentration in M for Generalized Born models
gb_saltconc              = 0

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent         = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                   = berendsen
; Groups to couple separately
tc-grps                  = System
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1
ref_t                    = 300
; Pressure coupling
Pcoupl                   = no
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 0.5
compressibility          = 4.5e-5
ref_p                    = 1.0
; Random seed for Andersen thermostat
andersen_seed            = 815131


Any idea about this problem? any suggestions will be highly appreciated .

Thank you .

Yang