[gmx-users] segmentation fault for unknown reason

gangotri dey holyriver6 at gmail.com
Wed Aug 2 21:23:19 CEST 2017


I am trying to minimize a periodic MnO2 surface using UFF force fields. I
have previously computed many structures using MnO2 clusters. I did not
face much problem.

However, when I am trying to compute the minimization using the following
minim.mdp there is segmentation error as follows.

; minim.mdp - used as input into grompp to generate em.tpr
integrator      = steep         ; Algorithm (steep = steepest descent
emtol           = 1000.0        ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps          = 50000         ; Maximum number of (minimization) steps to

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist             = 50                    ; Frequency to update the
neighbor list and long range forces
cutoff-scheme   = Verlet
ns_type             = grid              ; Method to determine neighbor list
(simple, grid)
coulombtype         = PME               ; Treatment of long range
electrostatic interactions
rcoulomb            = 1.0               ; Short-range electrostatic cut-off
rvdw                = 1.0               ; Short-range Van der Waals cut-off
pbc                     = xyz           ; Periodic Boundary Conditions


Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=    0, Dmax= 1.0e-02 nm, Epot=  3.46301e+34 Fmax= 2.91045e+06, atom=
[fen2.hpcc.rutgers.edu:mpi_rank_0][error_sighandler] Caught error:
Segmentation fault (signal 11)
./script: line 5: 54036 Segmentation fault      (core dumped) gmx_mpi mdrun
-ntomp 1 -v -deffnm em

I do not understand this problem. Is there anything wrong with my structure
or the minim.mdp?

*Thank you*

*Gangotri Dey*

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