title               =  cpeptide MD
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  50000	; total 100 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  0
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tau_t               =  0.1	0.1
tc-grps		    =  protein	sol
ref_t               =  300	300
; Pressure coupling is on
Pcoupl              =  berendsen
tau_p               =  5.0
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