constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  10000		; total 0.020 ns.
init_lambda			=  1
delta_lambda		=  -.0001
free_energy			=  yes
foreign_lambda		=  0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
nstdhdl				=  100
dhdl_derivatives	=  yes
separate_dhdl_file	=  yes
nstcomm             =  10
xtc_grps			=  Protein
nstxout             =  0
nstxtcout			=  100
nstvout             =  0
nstfout             =  0
nstlog              =  1000
nstenergy           =  10
nstcalcenergy		=  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
coulombtype			= PME
; velocity rescaling (correct ensemble) temperature coupling is on in two groups
Tcoupl              =  nose-hoover
nh-chain-length		=  1
tc-grps		    =  Protein	Non-protein
tau_t               =  0.5	0.5	; in v 4.5.3 tau_t should be at least 20X nstcouple (default = 10) * dt
ref_t               =  300	300
; Energy monitoring
energygrps          =  Protein  Non-protein
; Isotropic pressure coupling is now on
Pcoupl              =  Parrinello-Rahman
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529