in.peptide
d0bbf3fb9785efficient_neuronet

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

			#dump 2 peptide image 25 image.*.jpg type type &
			# axes yes 0.8 0.02 view 60 -30 bond atom 0.5
			#dump_modify 2 pad 3

			#dump 3 peptide movie 25 movie.mpg type type &
			# axes yes 0.8 0.02 view 60 -30 bond atom 0.5
			#dump_modify 3 pad 3

			#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