[gmx-users] segmentation fault during energy minimization

soumadwip ghosh soumadwipghosh at gmail.com
Fri Nov 28 19:22:04 CET 2014

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

;minim.mdp - used as input into grompp to generate em.tpr
integrator      = steep         ; Algorithm (steep = steepest descent
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
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
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
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)

Thanks and regards,
Soumadwip ghosh
research scholar,
IIT Bombay,

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