define		= -DPOSRES 
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 10005000	; 1ns
dt		= 0.001		; 1 fs
; Output control
nstxout		= 20		; save coordinates every 1 ps
nstvout		= 20		; save velocities every 1 ps
;nstxtcout	= 500		; xtc compressed trajectory output every 1 ps
nstenergy	= 100		; save energies every 1 ps
nstlog		= 500		; update log file every 1 ps
; Bond parameters
continuation	= no		; first dynamics run
constraint_algorithm = lincs	; holonomic constraints 
constraints	= h-bonds	; Convert the bonds with H-atoms to constraints
lincs_iter	= 1		; accuracy of LINCS
lincs_order	= 4		; also related to accuracy
; Neighborsearching
cutoff-scheme	= verlet
nstlist		= 10		; 10 fs
ns_type		= grid		; search neighboring grid cels
pbc		= xyz		; 3-D PBC
periodic-molecules = no
rlist		= 2.0		; short-range neighborlist cutoff (in nm)
; Van der Waals
rvdw		= 2.0		; 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
rcoulomb	= 2.0		; short-range electrostatic cutoff (in nm)
pme-order	= 4		; cubic interpolation
fourierspacing	= 0.12		; grid spacing for FFT
; Temperature coupling is on
tcoupl		= v-rescale	; More accurate thermostat
tc-grps		= system	; one group
tau_t		= 0.1		; time constant, in ps
ref_t		= 10		; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl		= no 		; no pressure coupling in NVT
; Velocity generation
gen_vel		= yes		; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the solvent/ions
nstcomm         = 10
comm-grps	= system
