title               =  2iis
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  2000000  
nstcomm             =  1
nstxout             =  500
nstvout             =  0
nstfout             =  0
nstlist             =  5
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  1.4
fourierspacing      = 0.075
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  0.1    
tc-grps             =  Protein  SOL  HEM  NA+
ref_t               =  498      498  498  498
; Pressure coupling is not on
Pcoupl              =  berendsen
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
;simulated annealing
annealing = single
annealing_npoints = 5 
annealing_time = 2 500 1000 1500 2000
annealing_temp = 300 350 400 450 450

; Time at which temperature should be zero (ps) = 
;zero-temp_time           = 0


; Generate velocites is on at 498 K.
gen_vel             =  yes
gen_temp            =  498.0
gen_seed            =  173529