title       = Umbrella pulling simulation 
;define      = -DPOSRES
; Run parameters
integrator  = md
dt          = 0.019
tinit       = 0
nsteps      = 500000   ; 9.5 ns 
nstcomm     = 10
; Output parameters
nstxout     = 500     ; every 9.5 ps
nstvout     = 500 
nstfout     = 500
nstxtcout   = 500      ; every 9.5 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm    = lincs
constraints             = none
continuation            = no 
; Single-range cutoff scheme
nstlist     = 5
ns_type     = grid 
rlist       = 1.4
rcoulomb    = 1.4
rvdw        = 1.4
; PME electrostatics parameters
coulombtype     = PME
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      = Nose-Hoover
tc_grps     = Protein   Non-Protein 
tau_t       = 2.1 2.1      
ref_t       = 310       310
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman 
pcoupltype      = isotropic
tau_p           = 2.1       
compressibility = 4.5e-5
ref_p           = 1.0
; Generate velocities is off
gen_vel     = no 
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
pull            = umbrella
pull_geometry   = distance
pull_dim        = N N Y
pull_start      = yes 
pull_ngroups    = 1
pull_group0     = non-protein 
pull_group1     = protein 
pull_init1      = 0
pull_rate1      = 0.0
pull_k1         = 1000      ; kJ mol^-1 nm^-2
pull_nstxout    = 100      ; every 2 ps
pull_nstfout    = 100      ; every 2 ps