; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 750000	; 2 * 750000 = 1500 ps
dt		= 0.002		; 2 fs
; Output control
nstxout		= 1000		; save coordinates every 0.2 ps
nstvout		= 1000		; save velocities every 0.2 ps
nstenergy	= 1000		; save energies every 0.2 ps
nstlog		= 1000		; update log file every 0.2 ps
;nstcalenergy    = 5            ; frequency for calculating energy; must be multiple of "nstlist"; will affect "nstdhdl"
; Bond parameters
continuation	= no		; 
constraint_algorithm = lincs	; holonomic constraints 
constraints	= h-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		= 1.30		; short-range neighborlist cutoff (in nm)
rcoulomb	= 1.30		; short-range electrostatic cutoff (in nm)

vdwtype		= Switch 
rvdw_switch	= 1.00
rvdw		= 1.20		; short-range van der Waals cutoff (in nm)

; Electrostatics
coulombtype	= PME		; Particle Mesh Ewald for long-range electrostatics
pme_order	= 4		; cubic interpolation
fourierspacing	= 0.10		; grid spacing for FFT
; Temperature coupling is on
tcoupl		= V-rescale	; modified Berendsen thermostat
tc-grps		= System	; two coupling groups - more accurate
tau_t		= 0.1		; time constant, in ps
ref_t		= 310 		; 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		= 1.01325		; reference pressure, in bar
compressibility = 4.5e-5	; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; 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 

;;>>>>>>>>>>>>>>> FREE ENERGY <<<<<<<<<<<<<<<<<<<<<<<<<<
free_energy              = yes
init_lambda              = MYLAMBDA0 
delta_lambda             = 0
foreign_lambda           = MYLAMBDA1
sc-alpha                 = 0.5
sc-power                 = 1.0
sc-sigma                 = 0.3
;#>>>>> GO FROM ONE SET OF PARAMETERS TO ANOTHER <<<<<<<<<<<
couple-moltype           = Other_chain_I    ; name of moleculetype to decouple
couple-lambda0           = vdw-q   ; elec + van der Waals interactions
couple-lambda1           = vdw    ; turn off everything, in this case only vdW
couple-intramol          = no
nstdhdl                  = 10  ; (20 fs) must be multiple of "nstcalenergy"
separate_dhdl_file       = yes   ; write  a separate file with FEP data