[gmx-users] segmentation fault during energy minimization

[Justin Lemkul]

On 11/28/14 1:21 PM, soumadwip ghosh wrote:
> Dear all,
>            I am stuck with the energy minimization of a 15 residue DNA
> single strand and every time I proceed for energy minimization, there
> isalways a segmentation fault. I am attaching the .mdp file and the error
> it is showing. Any kind of help regarding this problem will be highly
> appreciated.
>
> ;minim.mdp - used as input into grompp to generate em.tpr
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> emtol           = 10000.0       ; 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
> nstlist         = 1             ; Frequency to update the neighbor list and
> long range forces
> ns_type         = grid          ; Method to determine neighbor list
> (simple, grid)
> rlist           = 1.0           ; Cut-off for making neighbor list (short
> range forces)
> 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)
> ~
>
>
> And the fault it exhibits is something like this-
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+04
>     Number of steps    =        50000
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 10000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10000.
> Potential Energy  =  5.5140400e+30
> Maximum force     =            inf on atom 50
> Norm of force     =            inf
> [pople:13142] *** Process received signal ***
> Segmentation fault (core dumped)

Something is catastrophically wrong with the input structure.

-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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