; RUN CONTROL PARAMETERS = 
integrator               = md-vv
; start time and timestep in ps = 
tinit                    = 0
dt                       = 0.002
nsteps                   = 100000
; mode for center of mass motion removal = 
comm-mode                = Linear
; number of steps for center of mass motion removal = 
nstcomm                  = 1
nstcalcenergy            = 1
; group(s) for center of mass motion removal = 
comm-grps                = 


; OUTPUT CONTROL OPTIONS = 
; Output frequency for coords (x), velocities (v) and forces (f) = 
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
; Output frequency for energies to log file and energy file = 
nstlog                   = 2000
nstenergy                = 100000
; Output frequency and precision for xtc file = 
nstxtcout                = 1000000
xtc-precision            = 10000

; NEIGHBORSEARCHING PARAMETERS = 
; nblist update frequency = 
nstlist                  = 10
; ns algorithm (simple or grid) = 
ns_type                  = grid
; Periodic boundary conditions: xyz or no = 
pbc                      = xyz
; nblist cut-off         = 
rlist                    = 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW = 
; Method for doing electrostatics = 
coulombtype              = PME-Switch
rcoulomb-switch          = 0.88
rcoulomb                 = 0.90
; Dielectric constant (DC) for cut-off or DC of reaction field = 
epsilon-r                = 1
; Method for doing Van der Waals = 
vdw-type                 = Switch
; cut-off lengths        = 
rvdw-switch              = 0.80
rvdw                     = 0.90
; Apply long range dispersion corrections for Energy and Pressure = 
DispCorr                 = AllEnerPres
; Spacing for the PME/PPPM FFT grid = 
fourierspacing           = 0.10
; FFT grid size, when a value is 0 fourierspacing will be used = 
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters = 
pme_order                = 6
ewald_rtol               = 1e-06
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS = 
; Temperature coupling   = 
Tcoupl                   = Nose-Hoover

; Groups to couple separately = 
tc-grps                  = System
; Time constant (ps) and reference temperature (K) = 
tau_t                    = 5.0
nsttcouple               = 1
ref_t                    = 298
; Pressure coupling      = 
Pcoupl                   = MTTK
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) = 
tau_p                    = 5.0
nstpcouple               = 1
compressibility          = 4.5e-5
ref_p                    = 1.01325

; GENERATE VELOCITIES FOR STARTUP RUN = 
gen_vel                  = yes
gen_temp                 = 298
gen_seed                 = 12 

; OPTIONS FOR BONDS     = 
constraints              = all-bonds
; Type of constraint algorithm = 
constraint-algorithm     = shake
; Relative tolerance of shake = 
shake-tol                = 1e-12

; Free energy control stuff = 
free-energy               = yes
nstdhdl                   = 200
sc-power                  = 1
sc-alpha                  = 0.5
init-lambda-state         = FEP_STATE
coul-lambdas              = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.0 1.0 1.0 1.0  1.0 1.0  1.0 1.0  1.00 1.0 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.0  
vdw-lambdas               = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.2 0.3 0.35 0.4 0.45 0.5 0.55 0.58 0.6 0.62 0.64 0.66 0.68 0.70 0.72 0.74 0.76 0.78 0.80 0.82 0.84 0.86 0.88 0.92 0.96 1.0