title		=OPLS Lysozyme NVT equilibration
;define		=-DPOSRES       ;position restrain the protein
;Run parameters
integrator	=md		;leap-frog algorithm
nsteps		=50000		;2 * 50000 = 100 ps
dt		=0.002		;2fs
;Output control
nstxout		=100		;save coordinates every 0.2 ps
nstvout		=100		;save velocities every 0.2 ps
nstenergy	=100		;save energies every 0.2 ps
nstlog		=100		;update log file every 0.2 ps
;Bond parameters
continuation	=no		;first dynamics run
constraint_algorithm=lincs	;holonomic constraints
constraints	=all-bonds	;all bonds (even heavy atom-H bonds)constraind
lincs_iter	=1		;accuracy of LINCS
lincs_order	=4		;also related to accuracy
;Neighborhood searching
ns_type		=grid		;search neighboring grid cells
nstlist		=5		;10 fs
rlist		=1.0		;short-range neighborlist cutoff (in nm)
rcoulomb	=1.0		;short-range electrostatic cutoff (in nm)
rvdw		=1.0		;short-range van der Waals cutoff (in nm)
;Electrostatics	
coulombtype	=PME		;Particle Mesh Ewald for long-range electrostat;ics
pme_order	=4		;cubic interpolation
fourierspacing	=0.16		;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	;0.1		  ;time constant, in ps
ref_t		=298	;25		  ;reference temperature, one for each ;group, in K
;Pressure coupling is off
pcoupl	  	=no		;no pressure coupling in NVT
;Periodic boundary conditions
pbc	  	=xyz		; 3-D PBC
;Dispersion correction
DispCorr	=EnerPres	;account for cut-off vdW scheme
;Velocity generation
gen_vel		=yes		;assign velocities from Maxwell distribution
gen_temp	=25		;temperature for Maxwell distribution
gen_seed	=-1		;generate a random seed

;END