[gmx-users] Help with segmentation fault error

[Kunal Maniar]

Hi,

I have installed 5.1.1, and am trying to run the simulations. During the
run, I am getting this error as pasted below:
WARNING: Listed nonbonded interaction between particles 1 and 9
at distance 9.500 which is larger than the table limit 2.030 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


Segmentation fault (core dumped)

I have tried neutralizing the the charges, however, the error remains the
same. I am using the NVT parameters as below:
title        = OPLS Lysozyme NVT equilibration
define        = -DPOSRES    ; position restrain the protein
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 10000        ; 2 * 50000 = 100 ps
dt            = 0.002        ; 2 fs
; Output control
nstxout        = 1000        ; save coordinates every 1.0 ps
nstvout        = 1000        ; save velocities every 1.0 ps
nstenergy    = 1000        ; save energies every 1.0 ps
nstlog        = 1000        ; update log file every 1.0 ps
; Bond parameters
continuation            = no        ; first dynamics run
constraint_algorithm    = lincs        ; holonomic constraints
constraints                = all-bonds    ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter                = 1            ; accuracy of LINCS
lincs_order                = 4            ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type            = grid        ; search neighboring grid cells
nstlist            = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb        = 1.0        ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0        ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype        = PME    ; Particle Mesh Ewald for long-range
electrostatics
pme_order        = 4        ; cubic interpolation
fourierspacing    = 0.16    ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = V-rescale                ; modified Berendsen thermostat
tc-grps        = Protein Non-Protein    ; two coupling groups - more
accurate
tau_t        = 0.1      0.1           ; time constant, in ps
ref_t        = 300       300           ; reference temperature, one for
each group, in K
; Pressure coupling is off
pcoupl        = no         ; no pressure coupling in NVT
; Periodic boundary conditions
pbc        = xyz            ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = yes        ; assign velocities from Maxwell distribution
gen_temp    = 300        ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed

When using on an older Gromacs version (older than 5.1), the run is smooth
(everything else remaining constant). Can anyone help me to target the
error? Whether it is due my hardware issue (its a dell inspiron with 4 GB
RAM, i5 processor, 2 cores, 1.7 GHz) or I am making an error in the steps?

Thanks,
Kunal

-- 
Dr. Kunal Maniar
Resident,
Department of Pharmacology,
Post Graduate Institute of Medical Education and Research, Chandigarh
(PGIMER)
Mobile: +91 8968630447
Email id: drkunalmaniar at gmail.com