; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include                  =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define                   =

; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit = 0 
dt = 0.002 
nsteps = 4000000

; For exact run continuation or redoing part of a run
init-step                = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part          = 1
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 100
; group(s) for center of mass motion removal
comm-grps                =

; TEST PARTICLE INSERTION OPTIONS
rtpi                     = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 100000
; Output frequency for energies to log file and energy file
nstlog                   = 5000
nstcalcenergy            = 100
nstenergy                = 2500
; Output frequency and precision for .xtc file
nstxtcout                = 10000
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                 =
; Selection of energy groups
energygrps               = System

; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)
; nblist update frequency
cutoff-scheme            = Verlet
nstlist                  = 100
verlet-buffer-tolerance  = 0.0001
; ns algorithm (simple or grid)
ns_type                  = grid
; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
; nblist cut-off
rlist                    = 8.0
; long-range cut-off for switched potentials
rlistlong                = -1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = cut-off
rcoulomb-switch          = 0
rcoulomb                 = 8.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r                = 1
epsilon-rf               = 0
; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 8.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Separate tables between energy group pairs
energygrp-table          =
; IMPLICIT SOLVENT ALGORITHM
implicit-solvent         = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl                   = v-rescale
nsttcouple               = -1
nh-chain-length          = 1
; Groups to couple separately
tc-grps                  = System
; Time constant (ps) and reference temperature (K)
tau-t                    = 0.002
ref-t                    = 298.15
; pressure coupling
pcoupl                   = no
; Scaling of reference coordinates, No, All or COM
refcoord-scaling         = COM

; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel                  = yes
gen-temp                 = 500
gen-seed                 = 173529

; OPTIONS FOR BONDS
constraints              = h-bonds
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
continuation             = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = no
; Relative tolerance of shake
shake-tol                = 0.00001
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 5
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter               = 2
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle          = 50
; Convert harmonic bonds to morse potentials
morse                    = no