[gmx-users] Segmentation fault in MDRUN

[Matteo Busato]

Goodmorning,


I am trying to perform a very simple dynamic of an atom of Cu2+ in a box of tip3p water using the OPLS force field on GROMACS 5.0.4. I have done an energy minimization using the steepest algorythm and equilibrations in NVT and NPT ensemble, but during the mdrun of the dynamics I got a 'segmentation fault' and the system seems to blow up after 6 steps. This is the mdrun output:


starting mdrun 'Copper in water'
2500000 steps,   5000.0 ps.
step 0
step 2: Water molecule starting at atom 58 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

step 2: Water molecule starting at atom 58 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step2b.pdb to ./#step2b.pdb.1#

Back Off! I just backed up step2c.pdb to ./#step2c.pdb.1#
Wrote pdb files with previous and current coordinates

step 3: Water molecule starting at atom 343 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

step 3: Water molecule starting at atom 343 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step3b.pdb to ./#step3b.pdb.1#

Back Off! I just backed up step3c.pdb to ./#step3c.pdb.1#
Wrote pdb files with previous and current coordinates

step 4: Water molecule starting at atom 343 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

step 4: Water molecule starting at atom 343 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step4b.pdb to ./#step4b.pdb.1#

Back Off! I just backed up step4c.pdb to ./#step4c.pdb.1#
Wrote pdb files with previous and current coordinates

step 5: Water molecule starting at atom 343 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

step 5: Water molecule starting at atom 343 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step5b.pdb to ./#step5b.pdb.1#

Back Off! I just backed up step5c.pdb to ./#step5c.pdb.1#
Wrote pdb files with previous and current coordinates

step 6: Water molecule starting at atom 343 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

step 6: Water molecule starting at atom 343 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step6b.pdb to ./#step6b.pdb.1#

Back Off! I just backed up step6c.pdb to ./#step6c.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault (core dump creato)

THIS IS MY .MDP FILE FOR THE DYNAMICS:

; Run control
integrator               = sd       ; Langevin dynamics
dt                       = 0.002
nsteps                   = 2500000    ; 5 ns
nstcomm                  = 100
; Output control
nstxout                  = 1000
nstvout                  = 1000
nstfout                  = 1000
nstlog                   = 1000
nstenergy                = 1000
nstxout-compressed       = 1000
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme            = verlet
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 0.8
; Electrostatics
coulombtype              = PME
rcoulomb                 = 1.2
; van der Waals
vdwtype                  = cutoff
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; EWALD/PME/PPPM parameters
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tcoupl                   = Nose-Hoover
tc_grps                  = system
tau_t                    = 1.0
ref_t                    = 298.15
; Pressure coupling is on for NPT
Pcoupl                   = Parrinello-Rahman
tau_p                    = 0.5
compressibility          = 4.5e-05
ref_p                    = 1.0
refcoord_scaling         = com           ; centre of mass
; Free energy control stuff
; Generate velocities to start
gen_vel                  = no
gen_temp                 = 298.15
gen_seed                 = -1
; options for bonds
constraints              = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm     = lincs
; Do not constrain the starting configuration
continuation             = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 4
lincs-iter               = 1

THIS IS MY TOPOLOGY FILE:

; Topology for Copper in SPCE

#include "oplsaa.ff/forcefield.itp"

; water topology

#include "oplsaa.ff/spce.itp"

;Cu topology

[ moleculetype ]
; molname   nrexcl
CU          1

[ atoms ]
; id    at type res nr  residu name at name  cg nr  charge   mass
1       Cu2+    1       CU          CU       1      2        63.54600


[ system ]
; Name
Copper in water

[ molecules ]
; Compound             #mols
SOL                    1000
Cu                     1

I've already read the material in the web for this 'segmentation fault', but every single case seems to be different. In addition, I'm wondering if it could be a bug or just a simple blowing up. Sorry if I wrote something unsophisticated, but I am a new gromacs user. Thank you in advance.

Matteo Busato