# VARIAES
variable fname index data.PA6_3M16cc
variable simname index PA6_3M16cc

# Initialization
units		real			
boundary	p p p
atom_style	full
log 		log.${simname}.txt
read_data	${fname}

# Dreiding potential information

neighbor	0.4 bin			
neigh_modify	every 10 one 10000	

bond_style      harmonic
bond_coeff	1 1834.44 1.483 	# 1  C-C
bond_coeff	2 1515.82 1.535		# 2  C-C2
bond_coeff	3 1453.42 1.074 	# 3  C-H
bond_coeff	4 1881.86 1.441 	# 4  C-N
bond_coeff	5 1370.18 1.357 	# 5  C2-N
bond_coeff	6 2442.40 1.210 	# 6  C2-O
bond_coeff	7 1950.02 1.008 	# 7  H-N

angle_style     cosine/squared
angle_coeff	1 165.64 121.68 	# 1  C-C-C
angle_coeff	2 165.64 121.68 	# 2  C-C-C2
angle_coeff	3 127.96 118.21 	# 3  C-C-H
angle_coeff	4 165.64 121.68 	# 4  C-C-N
angle_coeff	5 95.20 119.24 		# 5  C-C2-N
angle_coeff	6 329.58 122.18 	# 6  C-C2-O
angle_coeff	7 518.10 112.11		# 7  C-N-C2
angle_coeff	8 152.04 98.43		# 8  C-N-H
angle_coeff	9 200.96 106.48		# 9  C2-C-H
angle_coeff	10 226.50 109.48	# 10  C2-N-H
angle_coeff	11 108.24 119.64	# 11  H-C-H
angle_coeff	12 244.30 104.12	# 12  H-C-N
angle_coeff	13 108.24 119.64	# 13  H-N-H
angle_coeff	14 409.06 120.09	# 14  N-C2-O

dihedral_style	harmonic
dihedral_coeff	1 5.70 1 0	# 1  C-C-C-C
dihedral_coeff	1 5.70 1 3
dihedral_coeff	2 5.70 1 0	# 2  C-C-C-C2
dihedral_coeff	2 5.70 1 3
dihedral_coeff	3 6.16 1 0	# 3  C-C-C-H
dihedral_coeff	3 6.16 1 3
dihedral_coeff	4 5.70 1 0	# 4  C-C-C-N
dihedral_coeff	4 5.70 1 3
dihedral_coeff	5 -1.34 1 0	# 5  C-C-C2-N
dihedral_coeff	5 24.62 1 1
dihedral_coeff	5 -1.94 1 2
dihedral_coeff	5 -4.68 1 3
dihedral_coeff	5 1.26 1 4
dihedral_coeff	5 -0.20 1 5
dihedral_coeff	5 0.14 1 6
dihedral_coeff	6 0 1 0		# 6  C-C-C2-O
dihedral_coeff	7 -5.32 1 0	# 7  C-C-N-C2
dihedral_coeff	7 1.56 1 1
dihedral_coeff	7 7.34 1 2
dihedral_coeff	7 -0.52 1 3
dihedral_coeff	7 1.28 1 4
dihedral_coeff	7 -0.28 1 5
dihedral_coeff	7 0.18 1 6
dihedral_coeff	8 0 1 0		# 8  C-C-N-H
dihedral_coeff	9 24.76 1 0	# 9  C-C2-N-C
dihedral_coeff	9 -25.76 1 2
dihedral_coeff	10 24.76 1 0	# 10  C-C2-N-H
dihedral_coeff	10 -15.76 1 2
dihedral_coeff	11 1.10 1 0	# 11  C2-C-C-H
dihedral_coeff	11 1.10 1 3
dihedral_coeff	12 5.70 1 0	# 12  H-C-C-H
dihedral_coeff	12 5.70 1 3
dihedral_coeff	13 6.16 1 0	# 13  H-C-C-N
dihedral_coeff	13 6.16 1 3
dihedral_coeff	14 0 1 0	# 14  H-C-C2-N
dihedral_coeff	15 0 1 0	# 15  H-C-C2-O
dihedral_coeff	16 0 1 0	# 16  H-C-N-C2
dihedral_coeff	17 0 1 0	# 17  H-C-N-H
dihedral_coeff	18 24.76 1 0	# 18  O-C2-N-C
dihedral_coeff	18 -20.50 1 2
dihedral_coeff	19 24.76 1 0	# 19  O-C2-N-H
dihedral_coeff	19 -17.80 1 2

improper_style harmonic
improper_coeff * 50 0.0

pair_style	lj/cut/coul/cut 9
pair_coeff	1 1 0.0792 3.423 9	# C-C
pair_coeff	1 2 0.0792 3.423 9	# C-C2
pair_coeff	1 3 0.0398 3.123 9	# C-H
pair_coeff	1 4 0.0783 3.344 9	# C-N
pair_coeff	1 5 0.0871 3.229 9	# C-O
pair_coeff	2 2 0.0792 3.423 9	# C2-C2
pair_coeff	2 3 0.0398 3.123 9	# C2-H
pair_coeff	2 4 0.0783 3.344 9	# C2-N
pair_coeff	2 5 0.0871 3.229 9	# C2-O
pair_coeff	3 3 0.2821 2.972 9	# H-H
pair_coeff	3 4 0.0396 3.083 9	# H-N
pair_coeff	3 5 0.0280 2.689 9	# H-O
pair_coeff	4 4 0.0553 3.173 9	# N-N
pair_coeff	4 5 0.0466 2.976 9	# N-O
pair_coeff	5 5 0.0667 3.005 9	# O-O


#####################################################
# Energyminimization

dump 		1 all cfg 10 dump.min_*.cfg mass type xs ys zs
dump_modify	1 element C C H N O

velocity 	all create 293 1231				
reset_timestep	0
fix 		2 all nvt temp 293 293 100.0

thermo		10
thermo_style	custom step temp press

timestep	1
min_style	hftn
minimize	1e-25 1e-25 1000 40000
unfix		2
undump		1

#####################################################
# Equilibration Stage 1 (Langevin dynamics at 293 K)

dump 		1 all cfg 500 dump.eq1_*.cfg mass type xs ys zs

dump_modify	1 element C C H N O


fix		1 all nve/limit 0.05				

fix		2 all langevin 293 293 10.0 904297		
thermo_style	custom step temp press				 
thermo          100						
timestep	1						
run		50000						
unfix 1								
unfix 2								
write_restart 	restart.${simname}.eq1			

undump		1

###############################################################
# Equilibration Stage 2 (NPT dynamics at 293 K)

dump 		1 all cfg 1000 dump.eq2_*.cfg mass type xs ys zs
dump_modify	1 element C C H N O

fix		1 all npt temp 293 293 50 iso 0 0 1000 drag 2	

fix  		2 all momentum 1 linear 1 1 1	

thermo_style	custom step temp press	

timestep	0.5			

reset_timestep	0			
run		400000			
unfix 1					
unfix 2					
write_restart 	restart.${simname}.eq2

undump		1