title		=Methanol npt equilibration
;define		=-DPOSRES       ;position restrain the protein
;Run parameters
integrator	=md		;leap-frog algorithm
nsteps		=200000		;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	=yes		;Restarting after NVT
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		=1		;10 fs
rlist		=1.4		;short-range neighborlist cutoff (in nm)
rcoulomb	=1.4		;short-range electrostatic cutoff (in nm)
rvdw		=1.4		;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;	300		  ;reference temperature, one for each ;group, in K
;Pressure coupling is on
pcoupl	  	=Parrinello-Rahman	;Pressure coupling on in NPT
pcoupltype	=isotropic		;uniform scaling of box vectors
tau_p		=2.0			;time constant, in ps
ref_p		=1.0			;reference pressure, in bar
compressibility	=4.5e-5		;isothermal compressibility of h2O, 1/bar
;Periodic boundary conditions
pbc	  	=xyz		; 3-D PBC
;Dispersion correction
DispCorr	=EnerPres	;account for cut-off vdW scheme
;Velocity generation
gen_vel		=no		;Velocity generation is off
;gen_temp	=25		;temperature for Maxwell distribution
;gen_seed	=-1		;generate a random seed

;END