title			= MD 
; Run parameters
integrator		= md		; leap-frog integrator
nsteps			= 500000	; 2 * 500000 = 1000 ps, 1 ns
dt			= 0.002		; 2 fs
; Output control
nstxout			= 1000		; save coordinates every 2 ps
nstvout			= 1000		; save velocities every 2 ps
nstxtcout		= 1000		; xtc compressed trajectory output every 2 ps
nstenergy		= 1000		; save energies every 2 ps
nstlog			= 1000		; update log file every 2 ps
; Bond parameters
continuation		= yes		; Restarting after NPT 
constraint_algorithm 	= lincs		; holonomic constraints 
constraints		= all-bonds	; all bonds (even heavy atom-H bonds) constrained
lincs_iter		= 1		; accuracy of LINCS
lincs_order		= 4		; also related to accuracy
; Neighborsearching
ns_type			= grid		; search neighboring grid cells
nstlist			= 5		; 10 fs
rlist			= 1.0		; short-range neighborlist cutoff (in nm)
rcoulomb		= 1.0		; short-range electrostatic cutoff (in nm)
rvdw			= 1.0		; short-range van der Waals cutoff (in nm)
; 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 on
tcoupl			= V-rescale		; modified Berendsen thermostat
tc-grps			= Protein Non-Protein	; two coupling groups - more accurate
tau_t			= 0.1	0.1	; time constant, in ps
ref_t			= 300 	300	; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl			= Parrinello-Rahman	; Pressure coupling on in NPT
pcoupltype		= isotropic		; uniform scaling of box vectors
tau_p			= 2.0		; time constant, in ps
ref_p			= 1.0		; reference pressure, in bar
compressibility 	= 4.5e-5	; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc			= xyz		; 3-D PBC
; Dispersion correction
DispCorr		= EnerPres	; account for cut-off vdW scheme
; Velocity generation
gen_vel			= no		; Velocity generation is off