# ----------------------------- Initialization Section --------------------

include      "system.in.init"        # specify the style of force field used


# ----------------------------- Atom Definition Section -------------------

read_data    "polymer_graphene.data"           # load atom coordinates and topology


# ----------------------------- Settings Section --------------------------

include      "system.in.settings"    # load the force field parameters

# ----------------------------- Run Section -------------------------------

# Only the graphene atoms are immobile.
group		graphene type 1

# Use "neigh_modify" to turn off calculation of interactions between immobilized
# atoms.
neigh_modify 	exclude group graphene graphene
group		mobile subtract all graphene

compute		Tm mobile temp
compute		Tg graphene temp
compute		KEg graphene ke
compute		KEm mobile ke
thermo		500
thermo_style	custom time temp ke pe c_Tm c_KEm c_Tg c_KEg  	
fix		1 mobile nvt temp 500 500 100
fix		2 all shake 0.0001 20 0 t 2 3 4 
fix		3 mobile recenter INIT INIT INIT	# constrain polymer COM
dump		1 all custom 500 nvt.lammpstrj id type xu yu zu

timestep        1.0
run		500000

write_data  system_after_nvt.data