in.peptide
View Options

			# 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

			thermo_style multi
			thermo 50

			fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
			fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31

			group peptide type <= 12
			dump 1 peptide atom 10 dump.peptide

			compute bnd all property/local btype batom1 batom2
			dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]

			run 300

lammps/examples/peptide/in.peptide0409125c4690lammps-icms