; VARIOUS PREPROCESSING OPTIONS
title                    = Production Simulation
cpp                      = /lib/cpp

; RUN CONTROL PARAMETERS
integrator               = md
tinit                    = 0       ; Starting time
dt                       = 0.002   ; 2 femtosecond time step for integration
nsteps                   = 2500000 ; Make it 5 ns

; OUTPUT CONTROL OPTIONS
nstxout                  = 50000 ; Writing full precision coordinates every nanosecond
nstvout                  = 50000 ; Writing velocities every nanosecond
nstfout                  = 0     ; Not writing forces
nstlog                   = 2500  ; Writing to the log file every step
nstenergy                = 2500  ; Writing out energy information every step
nstxtcout                = 2500  ; Writing coordinates every 5 ps
energygrps               = Carb Water_and_ions

; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 5
ns-type                  = Grid
pbc                      = xyz
rlist                    = 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype              = Reaction-Field
rcoulomb                 = 1.4
epsilon_rf               = 78
epsilon_r                = 1
vdw-type                 = Cut-off
rvdw                     = 1.4

; Temperature coupling  
Tcoupl                   = V-rescale
tc-grps                  = Carb     Water_and_ions
tau_t                    = 0.1      0.1
ref_t                    = 300      300
; Pressure coupling     
Pcoupl                   = Berendsen
Pcoupltype               = Isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no

; OPTIONS FOR BONDS    
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = yes
lincs-order              = 4
lincs-iter               = 1
lincs-warnangle          = 30