[gmx-users] segmentation fault for unknown reason

[Justin Lemkul]

On 8/2/17 3:23 PM, gangotri dey wrote:
> Hello!
> 
> 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
> minimization)
> 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
> perform
> 
> ; 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
> (yes/no)
> 
> 
> Error:
> 
> 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=
> 289
> [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?
> 

It's either the coordinates or the force field parameters.  You have a 
configuration with an energy on the order of 10^34 kJ/mol, which is essentially 
infinite, so something is fundamentally flawed.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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