in.rhodo
576c6315c7f1efficient_neuronet

in.rhodo
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			# Rhodopsin model

			variable x index 1
			variable y index 1
			variable z index 1
			variable t index 100

			units real
			neigh_modify delay 5 every 1

			atom_style full
			bond_style harmonic
			angle_style charmm
			dihedral_style charmm
			improper_style harmonic
			pair_style lj/charmm/coul/long 8.0 10.0
			pair_modify mix arithmetic
			kspace_style pppm 1e-4

			read_data ../../bench/data.rhodo

			replicate $x $y $z

			fix 1 all shake 0.0001 5 0 m 1.0 a 232
			fix 2 all npt temp 300.0 300.0 100.0 &
			z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1

			special_bonds charmm

			thermo 100
			thermo_style multi
			timestep 2.0

			run $t