title	=CHARMM Methanol
;Run Parameters
integrator	=md	;leap-frog integrator
nsteps		=500000	;2*500000=1000ps, 1 ns
dt		=0.002	;2 fs
;Output control
nstxout		=1000	;save coordinates every 2ps
nstvout		=1000	;save velocities every 2 ps
nstxtcout	=1000	;xtc compressed trajectory output every 2 ps
nstenergy	=1000	;save energies every 2 ps
nstlog		=1000	;update log file every 2 ps
;Bond Parameters
continuation	=yes	;Restarting after NPT
constraint_algorithm	=lincs	    ;holonomic constraints
constraints		=all-bonds  ;all bonds (even heavy atom-H bonds) constr;ained
lincs_iter		=1	    ;accuracy of LINCS
lincs_order		=4	    ;also related to accuracy
;Neighborsearching
ns_type		=grid	;search neighboring grid cells
nstlist		=1	;10fs
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 electrostatics
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, on for each group, in K
;Pressure coupling is on
pcoupl	  =Parrinello-Rahman	;Pressure coupling on in NPT
pcoupltype			=isotropic	   ;uniform scaling of box vect;ors
tau_p				=2.0		   ;time constant, in ps
ref_p				=1.0		   ;reference pressure, in bar
compressibility			=4.5e-5		   ;isothermal compr of H2O, ba;r^(-1)
;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
;END