;Preprocessing options
cpp=/usr/bin/cpp -traditional
include= -I../top

; define lambda for restraints, if appplicable
;define= -Dfc_angle=0.0 -Dfc_dist=0.0 -Dfc_dihed=0.0 -DPOSRES -DPOSREFC=4.184

; RUN CONTROL PARAMETERS =
integrator               = steep
nsteps                   = 500
; Output frequency for energies to log file and energy file =
nstlog                   = 1
nstenergy                = 1

; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol                    = 3000 ;100
emstep                   = 0.005 ;0.01
; Max number of iterations in relax_shells =
niter                    = 20
; Number of correction steps to use for L-BFGS minimization
;nbfgscorr                = 10
;default
;lincs_iter               = 8

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 1
; ns algorithm (simple or grid) =
ns_type                  = grid ;simple
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.0
domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = pme
;rcoulomb-switch          = 0
rcoulomb                 = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r                = 1
; Method for doing Van der Waals =
vdw-type                 = Cut-off ;switch
; cut-off lengths        =
;rvdw-switch              = 0.8
rvdw                     = 1.0  ;0.9
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                  = EnerPres
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.1
; 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
epsilon_surface          = 0
optimize_fft             = no


freezegrps = Protein
freezedim = Y  Y Y 


; Energy monitoring
;energygrps          =  Protein SOL  ;System
;Energy group exclusions
;energygrp_excl     =  Protein Protein