[gmx-users] equilibration + Segmentation fault
ndhumal at andrew.cmu.edu
Sat Jun 5 04:05:35 CEST 2010
I am trying to equilibrate my system, ionic liquids. My simulations gets
stop immediately. I reduced the step size. I modified initial structure.
I changed the box size. I checked force field parameters. I am using
opls foce field. I repeated my energy minimization 2-3 times. I could not
solve the problem. Every time i am geting following error message.
step 0Warning: 1-4 interaction between 20 and 27 at distance 3.803 which
is larger than the 1-4 table size 2.400 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
or with user tables increase the table size
Can you tell me how to solve this problem.
Here I have pasted the eqilibration file.
title = cpeptid position restraining
cpp = /usr/bin/cpp
constraints = none
integrator = md
dt = 0.001 ; ps !
nsteps = 100000 ; total 1.0 ps.
nstcomm = 1
nstxout = 10000
nstvout = 10000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
vdwtype = cut-off
rcoulomb = 1.0
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
ref_t = 300
; Pressure coupling is on
Pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
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