[gmx-users] mdp file
He, Yang
yang.he at mavs.uta.edu
Thu Nov 6 18:15:08 CET 2008
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
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