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

[vivek sinha]

Hey Alex,
I was also having the same error from two days although my topology files
and mdp files were (I think) correct. Just two hours ago I corrected the
problem. I just changed the timestep from 0.002 to 0.0002 and it worked.
You can also try this.

Regards,
Vivek Sinha


On Fri, Jul 18, 2014 at 12:42 AM, Alexandre Barrozo <barrozo.ah at gmail.com>
wrote:

> 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
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