[gmx-users] mdrun crash

rahul dhakne rahuldhakne89 at gmail.com
Mon Feb 23 06:12:49 CET 2015

Dear Gromacs user,

I am running mdrun to minimize (energy minimization) my structure
co-ordinate, but every time it stuck by displaying following error
 Back Off! I just backed up em.log to ./#em.log.8#
Reading file em.tpr, VERSION 5.0.4 (single precision)
Using 1 MPI thread
Using 16 OpenMP threads

1 GPU detected:
  #0: NVIDIA Quadro K600, compute cap.: 3.0, ECC:  no, stat: compatible

1 GPU auto-selected for this run.
Mapping of GPU to the 1 PP rank in this node: #0

Setting the maximum number of constraint warnings to -1

Back Off! I just backed up em.trr to ./#em.trr.8#

Back Off! I just backed up em.edr to ./#em.edr.8#

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =        50000

WARNING: Listed nonbonded interaction between particles 51227 and 51230
at distance 8.421 which is larger than the table limit 2.000 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.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

step=       0, Dmax= 1.0e-02 nm, Epot=          nan Fmax= 2.79093e+14,
atom= 39526

Parameter file is following
; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 10   ; 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    = 1.4    ; Frequency to update the neighbor list and long range
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)
constraints     = none

Please provide the solution to fix this error.

Thanking you in advance.


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