[gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11

[Nilesh Dhumal]

Hello,

I am trying to equilibrate glucose in water using Gromacs
4.0.5 version.  I am geting the error immidiately after the mdrun starts
Warning: 1-4 interaction between 1 and 18 at distance 3.462 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
p0_4238:  p4_error: interrupt SIGSEGV: 11
Killed by signal 2.

Is the problem in mdp file?
Nilesh

Here is my pr.mdp file
title               =  cpeptid position restraining
cpp                 =  /usr/bin/cpp
constraints         =  none
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  200000      ; total 1.0 ps.
nstcomm             =  1
nstxout             =  10
nstvout             =  1000
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 = Berendsen
tau_t = 0.1
tc-grps  =system
ref_t =   350
; Pressure coupling is  on
Pcoupl              = Berendsen
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            =  350.0
gen_seed            =  173529