title		= NPT Equilibration  
define		= -DPOSRES	; position restrain the protein
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 500000	; 2 * 500000 = 1000 ps (1 ns)
dt		= 0.002		; 2 fs
; Output control
nstxout		= 100		; save coordinates every 0.2 ps
nstvout		= 100		; save velocities every 0.2 ps
nstenergy	= 100		; save energies every 0.2 ps
nstlog		= 100		; update log file every 0.2 ps
; Bond parameters
continuation	= yes		; Restarting after NVT 
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 cels
nstlist		= 5		; 10 fs
rlist		= 1.2		; short-range neighborlist cutoff (in nm)
rcoulomb	= 1.2		; short-range electrostatic cutoff (in nm)
rvdw		= 1.2		; 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		= Nose-Hoover		; More accurate thermostat
tc-grps		= Protein POPE SOL CL- 	; three coupling groups - more accurate
tau_t		= 0.1	0.1 0.1 0.1	   ; time constant, in ps
ref_t		= 323 	323 323 323	   ; reference temperature, one for each group, in K
; Pressure coupling is on 
pcoupl		= Parrinello-Rahman	; Pressure coupling on in NPT
pcoupltype	= semiisotropic		; uniform scaling of x-y box vectors, independent z
tau_p		= 5.0			; time constant, in ps
ref_p		= 1.0	1.0		; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5	4.5e-5	; isothermal compressibility, 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
; COM motion removal
; These options remove motion of the protein/bilayer relative to the solvent/ions
nstcomm         = 1
comm-mode       = Linear
comm-grps       = Protein POPE SOL CL-

; Type of constraint algorithm
constraint_algorithm     = lincs