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

; define lambda for restraints, if appplicable
define= -DPOSRES

; RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0
dt                       = 0.002
nsteps                   = 10000
; number of steps for center of mass motion removal =
nstcomm                  = 1

; 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                = 2000
; Output frequency and precision for xtc file =
nstxtcout                = 2000
xtc-precision            = 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
;xtc_grps             = Protein

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; 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


; Energy monitoring
energygrps          =  Protein SOL  Na   ;System

;OPTIONS FOR TEMPERATURE COUPLING
Tcoupl                   = nose-hoover 
tc_grps                  = Protein  SOL  Na
tau_t                    = 0.1      0.1     0.1
ref_t                    = 296.594     296.594     296.594
;OPTIONS FOR PRESSURE COUPLING
Pcoupl                   = No
tau_p                    = 0.5
compressibility          = 4.5e-05
ref_p                    = 1.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = yes
gen_temp                 = 296.594
gen_seed                 = -1

; OPTIONS FOR BONDS     =
constraints              = all-bonds  ;hbonds
; Type of constraint algorithm =
constraint-algorithm     = Lincs
; Do not constrain the start configuration =
unconstrained-start      = yes  ;no
; Relative tolerance of shake =
shake-tol                = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order              = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle          = 30
; Convert harmonic bonds to morse potentials =
morse                    = no