[gmx-users] Segmentation fault after warning regarding Listed nonbonded interaction

[Alexandre Barrozo]

Hi everybody,


I am trying to make a simulation of an enzyme containing a metal ion using
a dummy model for it. I have inserted all the parameters, generated the
topology, solvated the system, without any problem.

When I try to run a first equilibration, I get the following warning:



WARNING: Listed nonbonded interaction between particles 127 and 134*
at distance 3f which is larger than the table limit 3f 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.

*These particles are close to the dummy model for the metal. I believe the
problem might be related to that, but I had no problem in generating
topologies, or anything like that.


After that warning, I have a Segmentation fault.


Here is my mdp file for the test equilibration that I was trying:

define                  = -DPOSRES -DPOSRES_WATER       ; position restrain
the protein
; Run parameters
integrator              = md                            ; leap-frog
integrator
nsteps                  = 50000                         ; 2 * 50000 = 100 ps
dt                      = 0.001                         ; 1 fs
; Output control
nstxout                 = 500                           ; save coordinates
every 1.0 ps
nstvout                 = 500                           ; save velocities
every 1.0 ps
nstenergy               = 500                           ; save energies
every 1.0 ps
nstlog                  = 500                           ; update log file
every 1.0 ps
; Bond parameters
continuation            = no                            ; first dynamics run
; constraint_algorithm  = lincs                         ; holonomic
constraints
constraints             = none                          ; all bonds (even
heavy atom-H bonds) constrained
; Neighborsearching
cutoff-scheme           = Verlet
ns_type                 = grid                          ; search
neighboring grid cells
nstlist                 = 30                            ; 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           = 1       1                             ; 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        =  1                                    ; temperature for
Maxwell distribution
gen_seed        = -1                                    ; generate a random
seed



Any clue about what is going on?


Cheers,

Alex