title               =  n.pdb restraining
warnings            =  10
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.001	; ps !
nsteps              =  1000	; total 20.0 ps.
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  5
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  1.4
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               =  300     	300    300
; Pressure coupling is   on
Pcoupl              =  berendsen 
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529