in.peptide-spring
6864dfa2d184efficient_neuronet

in.peptide-spring
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			# Solvated 5-mer peptide

			units real
			atom_style full

			pair_style lj/charmm/coul/long 8.0 10.0 10.0
			bond_style harmonic
			angle_style charmm
			dihedral_style charmm
			improper_style harmonic
			kspace_style pppm 0.0001

			read_data data.peptide

			neighbor 2.0 bin
			neigh_modify delay 5

			timestep 2.0

			group peptide type <= 12
			group one id 2 4 5 6
			group two id 80 82 83 84
			group ref id 37
			group colvar union one two ref

			fix 1 all nvt temp 275.0 275.0 100.0 tchain 1

			fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
			fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0

			fix 2a ref setforce 0.0 0.0 0.0

			fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31

			#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
			#dump_modify 1 sort id

			variable sp equal f_3a+f_3b

			thermo_style custom step temp etotal pe ke epair ebond v_sp
			thermo 10


			run 100