in.peptide-colvars
4f41258f5d81lammm-master

in.peptide-colvars
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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

			shell "rm -f out.colvars."
			fix 2 all colvars peptide.colvars
			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.colvar.lammpstrj id xu yu zu fx fy fz
			#dump_modify 1 sort id

			thermo_style custom step temp etotal pe ke epair ebond f_2
			thermo 10


			run 100

			run 100

			fix 2 all colvars peptide.colvars input out.colvars.state output out2

			run 100