[gmx-users] Gromacs is aborting without error during nvt equilibration

[Bodmer, Nicholas (bodmernk)]

I have been trying to run simulations in Gromacs and have recently changed to the Gromos force field with SPC water from Charmm27.

I am using the following equilibration script.
title           = NVT
define          = -DPOSRES      ; position restrain the protein
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 100000        ; 2 * 100000 = 200 ps
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 200           ; save coordinates every 0.4 ps
nstvout         = 200           ; save velocities every 0.4 ps
nstenergy       = 200           ; save energies every 0.4 ps
nstlog          = 200           ; update log file every 0.4 ps
; Bond parameters
continuation    = no            ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds) constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
vdw_type        = cut-off
rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME_Switch
rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = Protein Non-Protein   ; two coupling groups - more accurate
tau_t           = 0.1   0.1     ; time constant, in ps
ref_t           = 300   300     ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl          = no            ; no pressure coupling in NVT
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = yes           ; assign velocities from Maxwell distribution
gen_temp        = 300           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed


No matter what platform I try running on, Gromacs keeps aborting the run but is not giving me an error message of any kind, so I don't know why it is terminating.  Here are the last few lines from my log.



DD  step 56399 load imb.: force  3.2%  pme mesh/force 0.544

           Step           Time         Lambda
          56400      112.80000        0.00000

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    2.87690e+03    1.59156e+03    5.97234e+02    5.25491e+01    3.30048e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
    1.20223e+05   -2.13895e+03   -8.53415e+05   -7.64994e+04    9.90360e+02
      Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
   -7.72717e+05    1.33982e+05   -6.38734e+05   -7.59989e+05    2.99951e+02
 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -1.26840e+02   -1.75550e+02    2.56042e-05

DD  step 56599 load imb.: force  2.4%  pme mesh/force 0.548

           Step           Time         Lambda
          56600      113.20000        0.00000

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    2.87790e+03    1.52116e+03    6.47247e+02    7.01118e+01    3.30355e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
    1.18624e+05   -2.13895e+03   -8.51310e+05   -7.64871e+04    9.59061e+02
      Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
   -7.72201e+05    1.34063e+05   -6.38139e+05   -7.59997e+05    3.00131e+02
 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -1.26840e+02   -1.08145e+02    2.64497e-05

Can anyone clue me in on what might be causing the problem here?

Thanks,

Nick