define                  = -DFLEXIBLE
integrator              = md        ; leap-frog integrator
nsteps                  = 1000    ; 1 * 500000 = 50 ps
dt                      = 0.001     ; 0.5 fs
nstxout                 = 100       ; save coordinates every 1.0 ps
nstenergy               = 100       ; save energies every 1.0 ps
nstlog                  = 100       ; update log file every 1.0 ps

; Bond parameters
continuation            = no        ; first dynamics run
constraint_algorithm    = lincs     ; holonomic constraints
constraints             = h-bonds   ; bonds involving H are constrained
lincs_iter              = 1         ; accuracy of LINCS
lincs_order             = 4         ; also related to accuracy
; Nonbonded settings
cutoff-scheme           = Verlet    ; Buffered neighbor searching
ns_type                 = grid      ; search neighboring grid cells
nstlist                 = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb                = 0.9613990804113833       ; short-range electrostatic cutoff (in nm)
rvdw                    = 0.9613990804113833       ; short-range van der Waals cutoff (in nm)
DispCorr                = EnerPres  ; account for cut-off vdW scheme
; Electrostatics
coulombtype             = PME       ; Particle Mesh Ewald for long-range electrostatics
pme_order               = 4         ; cubic interpolation
fourierspacing          = 0.16      ; grid spacing for FFT
; Temperature coupling is off
tcoupl                  = no             ; no temperature coupling in NVE
; Pressure coupling is off
pcoupl                  = no        ; no pressure coupling in NVE
; Periodic boundary conditions
pbc                     = xyz       ; 3-D PBC
; Velocity generation
gen_vel                 = no       ; Velocity generation is off