; ==============================================================
; PREPORCESSING
; ==============================================================
title		= NVE ensemble + Truncation of NB interactions	; -
cpp		= /lib/cpp					; -
include		= -I /home/nsapay/gromacs/ffcharmm27 		; -

; ==============================================================
; RUN CONTROL 
; ==============================================================
; Integration ..................................................
integrator	= md   						; Algorithm (cg = conjugate gradient)
tinit		= 0						; Starting time	
dt		= 0.0001					; time step in ps
nsteps		= 1					; number of step to integrate
init_step	= 0						; starting step
; System .......................................................
comm_mode	= Angular					; COM motion
nstcomm		= 10						; frequency for COM motion removal
comm_grps	= System					; group(s) for COM removal
; Output control ...............................................
nstxtcout	= 1					; Write coordinates
nstvout         = 1					; Write velocities
nstfout		= 1					; Write forces
nstlog		= 1					; Write energies in the log file
nstenergy	= 1					; Write energies in the energy file
xtc_grps	= System  					; Which coordinate group(s)
energygrps	= System  					; Which energy group(s)

; ==============================================================
; NEIGHBOR SEARCHING
; ==============================================================
nstlist		= 10						; Frequency to update the neighbor list
ns_type		= simple					; Method to determine neighbor list
pbc		= no						; Periodic Boundary Conditions
rlist		= 5.0					; Cut-off for the short range neighbor list

; ==============================================================
; NON-BONDED INTERACTIONS
; ==============================================================
; Electrostatics ...............................................
coulombtype	= Cut-off   				  	; Treatment of long range electrostatics
rcoulomb	= 5.0					; long range electrostatic cut-off
; van der Waals ................................................
vdwtype		= Cut-off					; Treatment of the long range LJ interactions
rvdw		= 5.0					; Long range Van der Waals cut-off

; ==============================================================
; BONDED INTERACTIONS
; ==============================================================
constraints		= none					; -
unconstrained_start     = yes					; -
constraint_algorithm 	= shake					; -
shake_tol		= 0.0001				; -
morse			= no					; Bonds are represented by a harmonic potential

; ==============================================================
; TEMPERATURE 
; ==============================================================
tcoupl		= no						; Treatment of the temperature

; ==============================================================
; PRESSURE 
; ==============================================================
pcoupl		= no						; Treatment of the pressure

; ==============================================================
; VELOCITY GENERATION 
; ==============================================================
gen_vel		= no						; Generate velocities at startup
gen_temp	= 298.0					; temperature for Maxwell distribution
gen_seed	= 51						; -