# Minimize a structure


# 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_data	6na_nma2.data.txt # change input according to your data file
#read_restart    restart.3343.min 


# Settings
neighbor        2.0 bin
neigh_modify	delay 0 every 1 check yes
timestep        1
kspace_style 	pppm 0.00001
#fix 		hbond all shake 1E-8 20000 0 m 1.008 m 2.014 a 4


# Running and Output

variable dens equal "(mass(all) / vol)"
thermo_style    custom step temp epair emol pe ke etotal press vol v_dens 
thermo			100
dump			12 all xyz 100 dump.min.xyz 
dump_modify             12 sort id  element  O H Na Cl C H1 C O N H2 
restart			50 restart.*.min	


min_style		cg
minimize		1.0e-8 1.0e-8 2500 100000
min_style		sd
minimize		1.0e-9 1.0e-9 4500 500000
min_style		cg
minimize		0.0 0.0 4000 500000