# Defrost/NPT ensemble

# Initialization
units			real
atom_style		full
boundary        p p p
  
# Atom Definition
pair_style      lj/cut/coul/long 12
pair_modify     shift yes
pair_modify 	mix arithmetic
special_bonds 	lj 0.000000 0.000000 0.500000
special_bonds 	coul 0.000000 0.000000 0.833300
bond_style 	harmonic
angle_style 	harmonic
dihedral_style 	charmm
improper_style 	cvff


read_restart		restart.4050.min #Change to latest restart file
velocity		all create 5.0 4928459 rot yes dist gaussian


# Settings
neighbor        2.0 bin
neigh_modify    delay 0 every 1 check yes
timestep        2
kspace_style 	ewald 0.00001

# GROUPINGS (Select all that apply)
#fix spce if have water in system, hbond for other systems
 fix spce all shake 1E-8 20000 0  b 1 a 1
#fix hbond all shake 1E-8 20000 0 m 1.0
#fix hbond all shake 1E-8 20000 0 m 2.014 m 1.008 

compute bond all pe bond
compute angle all pe angle
compute dihedral all pe dihedral
compute improper all pe improper
compute kspace all pe kspace
compute pe all pe
#fix potential all ave/time 1 1 50 c_bond c_angle c_dihedral c_improper c_kspace c_pe ave one file potential-defnpt.data


# Running and Output
variable dens equal "1.660538863*(mass(all) / vol)"
thermo_style    custom step temp epair emol pe ke etotal press vol enthalpy v_dens
thermo			50
dump			12 all custom 25 dump.def-npt.xyz id mol type x y z #xu yu zu
dump_modify		12 sort id  element   O H Na Cl C H1 C O N H2
restart			50 A-def-npt.restart B-def-npt.restart

fix				1 all nvt temp 5.0 300.0 500.0 #temp values Tstart Tstop Tdamp
run				50000 # 100ps of runtime in NVT ramping up temp
unfix			1

fix				1 all nvt temp 300.0 300.0 500.0
run				50000 # 100ps of runtime in NVT constant temp
unfix			1

fix				mynpt all npt temp 300.0 300.0 500.0 iso 1.0 1.0 500.0
compute			mytemp all temp #iso = Pstart,Pstop are scalar external pressure Pdamp=pressure damping param(time units)
compute 		mypress all pressure mytemp
run				2400000 # 4.8ns of runtime in at constant temperature
unfix			mynpt