;PREPROCESSING STEPS
title	 		= 			; TITLE OF THE RUN
cpp			= /lib/cpp		; C-PREPROCESSOR PATH

;RUN CONTROL
integrator		= md			; ALGORITH USED FOR INTEGRATION - LEAP FROG
tinit			= 0			; STARTING TIME FOR MD
dt			= 0.002			; TIME STEP FOR RUN - 2 FS
nsteps			= 5000000		; MAXIMUM NUMBER OF STEPS TO INTEGRATE - 10 NS
nstcomm			= 10			; FREQUENCY OF CENTRE OF MASS REMOVAL

;OUTPUT CONTROL
nstxout			= 1000			; FREQUENCY TO WRITE THE OUTPUT TRAGECTORY FILE
nstvout			= 1000			; FREQUENCY TO WRITE VELOCITIES TO OUTPUT TRAJECTORY
nstfout			= 0 0			; FREQUENCY TO FORCES TO OUTPUT TREJECTORY
nstlog			= 1000			; FREQUENCY TO WRITE ENERGIES TO LOG FILE
nstenergy		= 1000			; FREQUENCY TO WRITE ENERGY TO ENERGY FILE
nstxtcout		= 1000 			; FREQUENCY TO WRITE COORDINATES TO XTC TRAJECTORY
energygrps		= protein non-protein 	; GROUPS WRITEN TO ENERGY FILE

;NEIGHBOURSEARCHING PARAMETERS
nstlist			= 10 10			; FREQUENCY WITH WHICH NEIGHBOURLIST IS UPDATED
ns_type			= grid			; TYPE OF NEIGHBOUR SEARCH GRID OR SIMPLE
pbc			= xyz			; DIRECTION OF PERIODIC BOUNDARY CONDITIONS USAGE
rlist			= 1.4			; CUT-OFF DISTANCE FOR SHORT RANGE NEIGHBOUR LIST

;ELECTROSTATICS
coulombtype    	 	= PME    	 	; METHOD FOR CALCULATING COULOMBIC INTERCATION - PME
rcoulomb       		= 1.4                  	; CUTOFF DISTANCE FOR ELECTROSTATIC INTERACTIONS
epsilon_r     		= 1              	; RELATIVE DIELECTRIC CONSTANT

;VAN DER WAALS
vdwtype       		= Switch           	; METHOD FOR TREATING VANDERWAAL'S FORCES
rvdw_switch    		= 0.9			; WHEN TO START SWITCHING LJ POTENTIAL	
rvdw           		= 1.0                  	; CUTOFF DISTANCE FOR LJ OR BUCKINGHAM INTERACTIONS

;EWALD
fourierspacing 		= 0.12                  ; GRID SPACING FOR FFT GRID FOR PME
pme_order		= 4            	        ; INTERPOLATION ORDER FOR PME
ewald_rtol		= 1e-5         	 	; RELATIVE STRENGTH OF EWALD SHIFTED DIRECT POTENTIAL
optimize_fft		= yes			; SAVES A FEW PERCENT FOR LONG SIMULATIONS

;TEMPERATURE COUPLING
Tcoupl			= nose_hoover		; METHOD USED FOR TEMPERATURE COUPLING
tc_grps			= Protein Non-Protein	; GROUPS TO COUPLE SEPERATELY TO TEMPERATURE BATH
tau_t			= 0.4     0.4		; TIME CONSTANT IN PS
ref_t			= 300	  300		; REFERENCE TEMPERATURE IN KELVIN
nh-chain-length         = 1                     ; NO. OF CHAINED NOSE-HOOVER THERMOSTAT

;PRESSURE COUPLING
pcoupl			= parrinello_rahman	; METHOD FOR PRESSURE COUPLING
pcoupltype		= isotropic		; DIRECTIONALITY OF PRESSURE COUPLING
tau_p			= 2.0			; TIME CONSTANT IN PS
compressibility		= 4.5e-5		; COMPRESSIBILITY (1/BAR)
ref_p			= 1.0			; REFERENCE PRESSURE in BAR

;VELOCITY GENERATION
gen_vel                 = no                    ; GENERATES VELOCITY ACCORDING TO MAXWELL-BOLTZMAN DISTRIBUTION

;BONDS	
continuation		= yes			; CONSTRAINT IN STARTING CONFIGURATION	
constraints		= all-bonds		; SUBJECT ALL BONDS TO CONSTRAINTS
constraint-algorithm	= LINCS			; ALGORITHM FOR CONSTRAINTS
lincs-order             = 4			; HIGHEST ORDER IN THE EXPANSION OF CONSTRAINT COUPLING
lincs-iter              = 1			; NO. OF ITERATION TO CORRECT FOR ROTATIONAL LENGTHENING IN LINCS
lincs-warnangle         = 30			; MAX. ANGLE A BOND CAN ROTATE BEFORE WARNING