git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11728 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/USER/colvars/in.peptide-spring

@@ -0,0 +1,44 @@
+# 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

examples/USER/colvars/in.peptide-spring2

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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		3  one spring couple two 100.0 0.0 0.0 0.0 10.0
+
+fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+
+#dump		1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
+#dump_modify 1  sort id
+
+thermo_style	custom step temp etotal pe ke epair ebond f_3
+thermo		10
+
+
+run		100