;================== run control ===================================
integrator		= sd
tinit			= 0 
dt			= 0.001		; time step [ps]
nsteps			= 40000		; number of steps
comm_mode		= Linear	; Remove center of mass translation
nstcomm			= 10		; reset c.o.m. motion
;================== Polarizable model parameters ======================= Same parameter for Energy minimization - WATCH OUT
emtol			= 0.001		; the convergency criterion for maximum force
niter			= 30		; maximum number of iterations for the shell particle optimization

;================== Output control ===================================
nstxout			= 0		; write coords
nstvout			= 0		; write velocities
nstfout			= 0		; do NOT write forces 

nstlog			= 1000		; print to logfile
nstenergy		= 1000

nstxtcout		= 0		; write coords to xtc-trajectory file
xtc-precision		= 1000

;================== Neighborsearching and short-range nonbonded interactions
nstlist			= 10		; update pairlist
ns_type			= grid		; pairlist method    
pbc			= xyz		; periodic boundary conditions
;periodic_molecules	= no
rlist			= 1.5		; cut-off for neighborsearching - rlist >= rvdw+ (0.1 till 0.3)
;rlistlong		= 1.5		; long-range neighbor search, used with switch
;================== Electrostatics
coulombtype		= PME
rcoulomb		= 1.5		; cut-off for coulomb - rcoulomb = rlist
fourierspacing		= 0.112 ; nm
pme_order		= 4
ewald_rtol		= 1e-05
;================== dispersion correction
dispcorr		= EnerPres
;================== Van der Waals
vdw-type            =  switch
rvdw_switch         =  1.0
rvdw                =  1.2              ; cut-off for vdw

;================== OPTIONS FOR WEAK COUPLING ALGORITHMS ===============
tc-grps			=  System 
ref_t			=  298.15 
tau_t			=  1.0
Pcoupl			=  no		; pressure bath (berendsen)
Pcoupltype		=  isotropic	; pressure geometry
tau_p			=  1.0		; p-coupoling time
compressibility		=  4.5e-5           
ref_p			=  1.01325 
;================== GENERATE VELOCITIES FOR STARTUP RUN =================
gen_vel			=  yes		; generate initial velocities
gen_temp		=  298.15	; initial temperature
gen_seed		=  -1		; random seed
continuation		=  no		; apply constraints and reset shells

;================== OPTIONS FOR BONDS ===================================   
constraints		= h-bonds
constraint_algorithm	= lincs
shake_tol		= 0.00001
lincs_order		= 4
lincs_warnangle		= 30
morse			= no
lincs_iter		= 2

;================== Free energy control stuff ===========================
free-energy		= yes
init-lambda		= 0.0
delta-lambda		= 0.00
foreign_lambda		= 0.167
sc-alpha		= 0.0		; soft core is turned off for Coulomb decoupling
sc-sigma		= 0.0
sc_power		= 1.0

couple-moltype		= solute	; name of moleculetype to decouple
couple-lambda0		= vdw-q		; all interactions are on at start
couple-lambda1		= vdw		; turn off coulomb interaction
couple-intramol		= no
nstdhdl			= 100

separate_dhdl_file	= yes