[gmx-users] box explodes after 13ns

[Belquis Mothana]

Dear Gromacs users,

I am running a 50ns simulations of the unbinding of two peptide strands,
the calculation runs smoothly but then after 13ns the box start to explode
for several ps and then it returns to normal size and this goes on. The
calculation doesn't crash. I am wondering if there is anything I should
change in my Mdp file so that my box doesn't explode?

here is my mdp file:

; RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0
dt                       = 0.002
nsteps                   = 25000000 ; 50ns
; number of steps for center of mass motion removal =
nstcomm                  = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 1000
nstvout                  = 1000
nstfout                  = 1000
; Output frequency for energies to log file and energy file =
nstlog                   = 1000
nstenergy                = 1000
; Output frequency and precision for xtc file =
nstxtcout                = 0
xtc-precision            = 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
;xtc_grps                 =
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.0
domain-decomposition     = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = pme
;rcoulomb-switch          = 0
rcoulomb                 = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r                = 1
; Method for doing Van der Waals =
vdw-type                 = switch
; cut-off lengths        =
rvdw-switch              = 0.8
rvdw                     = 0.9
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                  = EnerPres
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.1
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
optimize_fft             = no
;restraints
dihre=simple
dihre-fc=1
nstdihreout=1000
disre=simple
disre_fc=1
;OPTIONS FOR TEMPERATURE COUPLING
Tcoupl              =  berendsen
tc_grps                  = Protein Non-Protein
tau_t                    = 0.1 0.1
ref_t                    = 300 300
;OPTIONS FOR PRESSURE COUPLING
Pcoupl              =  berendsen
tau_p                    = 0.5
compressibility          = 4.5e-05
ref_p                    = 1.0
; Free energy control stuff
free_energy              = no
sc_alpha                 =0.5
sc-power                 =1.0
sc-sigma                 = 0.3
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = -1
; OPTIONS FOR BONDS     =
constraints              = all-bonds
; Type of constraint algorithm =
constraint-algorithm     = Lincs
; Do not constrain the start configuration =
unconstrained-start      = no
; Relative tolerance of shake =
shake-tol                = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order              = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle          = 30
lincs_iter               =4