[gmx-users] System blowing up in final MD run

[Deep Bhattacharya]

Hello,
My system is blowing up for the protein carbohydrate solvent complex. I
have attached the mdp file below. The NPT and NVT were in good accordance
to tutorial listed by Justin. 'Please help me solve the issue.
title       = CD44  complex MD simulation
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 10000000    ; 0.001 * 1000000 = 10000 ps (10 ns)
dt          = 0.001     ; 1 fs
; Output control
nstxout             = 50000         ; suppress .trr output
nstvout             = 50000         ; suppress .trr output
nstenergy           = 50000    ; save energies every 1000.0 ps
nstlog              = 50000      ; update log file every 1000.0 ps
nstxtcout = 50000
xtc_precision = 1000
energygrps          = Protein LIG SOL
; Bond parameters
continuation    = yes           ; 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         = 1        ;
rcoulomb        = 0.81
rvdw            = 0.81
coulombtype     = Cut-off       ; Particle Mesh Ewald for long-
vdwtype        = cut-off
rlistlong      = 1.4
epsilon-rf     = 61
rlist          = 0.8
; Temperature coupling is on
tcoupl = nose-hoover            ; modified Berendsen thermostat
tc-grps       =Protein_LIG Water_and_ions   ; two coupling groups - more
accurate
tau_t = 2.0  2.0        ; time constant, in ps
ref_t = 300  300        ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl        = Parrinello-Rahman            ; Pressure coupling on in NPT
pcoupltype        = isotropic            ; uniform scaling of box vectors
tau_p        = 6.0            ; time constant, in ps
ref_p        = 1.0            ; reference pressure, in bar
compressibility     = 4.5e-5            ; isothermal compressibility of
water, bar^-1
refcoord_scaling    = com
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no        ; assign velocities from Maxwell distribution


Steepest Descents converged to Fmax < 1000 in 573 steps
Potential Energy  = -7.58370311664555e+05
Maximum force     =  9.53896348096555e+02 on atom 1163
Norm of force     =  2.44608995242254e+01


*Deep S Bhattacharya*

*Graduate Research Assistant*

Mohs Biomedical Imaging & Nanotechnology Group

Pharmaceutical Sciences

*University of Nebraska Medical Center*

4018 Eppley Science Hall  |  Omaha, NE 68198-6805

office 402.559.4349  | cell 402.906.1640

deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com