; Intergrator, timestep, and total run time

integrator = md ; Leap-frog MD algorithm

dt = 0.001 ; Sets timestep at 1 fs
nsteps = 15000000 ; Sim will run 15 ns

; Logs and outputs

nstlog = 5000 ; Output to md.log every 5000 dt
nstenergy = 5000 ; Output to ener.edr every 5000 dt
nstxout-compressed = 2000 ; Output to trajj.trr every 5000 dt

; Bond constraints
continuation = yes
constraint-algorithm = lincs
constraints = h-bonds

; Van der Waals interactions

vdwtype = Cut-off ; Define type of short-ranged
interaction
rvdw = 1.2 ; Define short-ranged cutoff as 1 nm
cutoff-scheme = Verlet ; Generate pair lists to speed up
simulation
DispCorr = EnerPres ; Apply corrections to mitigate
using cutoff

; Coulombic interactions
coulombtype = PME ; Define type of long-ranged interactions
rcoulomb = 1.2 ; Define long-ranged cutoff as 1nm

; Thermostat
tcoupl = V-rescale ; Define type of thermostat
tc-grps = System ; Define groups to be affected by
thermostat
ref-t = 298.15 ; Define temperature for each group in
Kelvins
tau-t = 2.0 ; Define temperature coupling time

; Barostat
pcoupl = Parrinello-Rahman ; Define type of barostat
ref-p = 1.0 ; Define system pressure in bars
tau-p = 4 ; Define pressure coupling time
compressibility = 4.5e-5 ; Define compressibility of system
in bar^-1