in.rigid.tnr
efaa4c67109flammm-devel

in.rigid.tnr
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			# Tethered nanorods

			atom_style molecular

			read_data data.rigid.tnr

			# Specify bond parameters

			bond_style fene
			bond_coeff 1 30.0 1.5 1.0 1.0

			special_bonds fene

			# Specify initial velocities

			velocity all create 1.4 109345

			# Specify rigid components

			group rods type 2
			group tethers subtract all rods

			neigh_modify exclude molecule/intra rods delay 0 every 1

			# Specify the pair potentials

			pair_style lj/cut 2.5
			pair_modify shift yes
			pair_coeff * * 1.0 1.0 1.122
			pair_coeff 2 2 1.0 1.0 2.5

			# Specify output

			thermo 100
			thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
			thermo_modify flush yes lost warn

			timestep 0.005

			fix 1 rods rigid molecule
			fix 2 tethers nve
			fix 3 all langevin 1.4 1.4 1.0 437624

			run 5000

			# Replace fix rigid and fix langevin with new ones

			unfix 1
			unfix 3

			fix 3 tethers langevin 1.4 1.4 1.0 198450

			# Test different integrators for rods

			fix 1 rods rigid/nve molecule
			print "rigid/nve"
			run 1000
			unfix 1

			fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
			print "rigid/nvt"
			run 1000
			unfix 1

			compute myTemp all temp

			fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 &
			dilate all
			print "rigid/npt iso"
			fix_modify 1 temp myTemp

			run 1000
			unfix 1

			fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
			print "rigid/npt x"
			run 1000
			unfix 1

			fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
			print "rigid/nph iso"
			run 1000
			unfix 1

			fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 &
			couple xy dilate all
			print "rigid/nph xy couple"
			run 1000