em_real.mdp

; LINES STARTING WITH ';' ARE COMMENTS
title		= Minimization	; Title of run

; Parameters describing what to do, when to stop and what to save
integrator	= steep		; Algorithm (steep = steepest descent minimization)
emtol		= 1000.0  	; Stop minimization when the maximum force < 10.0 kJ/mol
emstep      = 0.01      ; Energy step size
nsteps		= 50000	  	; Maximum number of (minimization) steps to perform
energygrps	= Protein BNZ	; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist		= 1		    ; Frequency to update the neighbor list and long range forces
ns_type		= grid		; Method to determine neighbor list (simple, grid)
rlist		= 1.0		; Cut-off for making neighbor list (short range forces)
coulombtype	= PME		; Treatment of long range electrostatic interactions
rcoulomb	= 1.0		; long range electrostatic cut-off
rvdw		= 1.0		; long range Van der Waals cut-off
pbc		    = xyz 		; Periodic Boundary Conditions (yes/no)