define            =        -DFLEXIBLE
ttle             =          LD5
cpp               =        /usr/bin/cpp
constraints       =          all-bonds 
integrator        =          md 
dt                =          0.002
nsteps            =          5000
nstcomm           =          1
nstxout           =          500
nstvout           =          0
nstfout           =          0
nstlist           =          5
ns_type           =          grid
rlist             =         1.0
coulombtype       =         PME
rcoulomb          =         1.0
rvdw              =         1.2
fourierspacing  ` =         0.12
fourier_nx        =          0
fourier_ny        =          0
fourier_nz        =          0
pme_order         =          4 
ewald_rtol        =          1e-5
optimize_fft      =          yes

; Berendsen temperature coupling is on in two groups
Tcoupl    =          berendsen
tau_t     =          0.1       0.1     0.1
tc-grps   =        protein     sol     NA+
ref_t     =          325       325     325


;pressure coupling is on 
Pcoupl           =          berendsen
tau_p            =          10.0
compressibility  =          4.5e-5
ref_p            =          3.0

;generate velocities is on at 300K.
gen_vel           =          yes
gen_temp          =          300.0
gen_seed          =          173529