title		= Equilibration MD according to Piggot2012.
; define		= -DPOSRES
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 50000	; 2 * 50000 = 100 ps (100 ps)
dt		= 0.002		; 2 fs
; Output control
nstxout		= 500000	; save trr-coordinates every 1000 ps
nstvout		= 500000	; save velocities every 1000 ps
nstfout		= 500000	; save forces every 1000 ps
nstxtcout	= 500		; save xtc-coordinates every 1 ps
nstenergy	= 5000		; save energies every 10 ps
nstlog		= 5000		; update log file every 10 ps
energygrps	= Other	        ; save energies of membrane
; Bond parameters
continuation	= no		; No restart
constraint_algorithm = lincs	; holonomic constraints 
constraints	= all-bonds	; hydrogen 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 ; was 1.0		; short-range neighborlist cutoff (in nm) !!!DIFF
rlistlong       = 1.4 ; was 1.6
rcoulomb	= 1.2 ; was 1.0		; short-range electrostatic cutoff (in nm) !!!DIFF
vdw-type        = switch
rvdw-switch     = 1.2 ; was 0.8
rvdw		= 1.4 ; was 1.5		; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype	= PME		; Particle Mesh Ewald for long-range electrostatics
pme_order	= 4		; cubic interpolation
fourierspacing	= 0.12		; grid spacing for FFT
; Temperature coupling is on
tcoupl		= V-rescale				; More accurate thermostat
tc-grps		= Protein POPC	SOL	; three coupling groups - more accurate
tau_t		= 0.1	0.1	0.1		; time constant, in ps 
ref_t		= 310   310	310		; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl		= Berendsen	; Pressure coupling on in NPT
pcoupltype	= semiisotropic		; uniform scaling of x-y-z box vectors
tau_p		= 1.0 1.0			; time constant, in ps
ref_p		= 1.013	1.013		; reference pressure (in bar)
compressibility = 4.5e-5	4.5e-5	; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc		= xyz		; 3-D PBC
; Dispersion correction
DispCorr	= No	; do not account for cut-off vdW scheme !!!DIFF
; Velocity generation
gen_vel		= yes		; Velocity generation is off
gen_temp        = 310           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed