From 4f41258f5d817a9ceed431eb06577872676552db Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 7 Apr 2014 19:46:46 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11728 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/USER/colvars/in.peptide-spring | 44 ++++++++++++++++++++++++ examples/USER/colvars/in.peptide-spring2 | 39 +++++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 examples/USER/colvars/in.peptide-spring create mode 100644 examples/USER/colvars/in.peptide-spring2 diff --git a/examples/USER/colvars/in.peptide-spring b/examples/USER/colvars/in.peptide-spring new file mode 100644 index 0000000000..89f32c783c --- /dev/null +++ b/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 diff --git a/examples/USER/colvars/in.peptide-spring2 b/examples/USER/colvars/in.peptide-spring2 new file mode 100644 index 0000000000..47d94c9df6 --- /dev/null +++ b/examples/USER/colvars/in.peptide-spring2 @@ -0,0 +1,39 @@ +# 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