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Merge pull request #288 from akohlmey/moltemplate-1.40
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Authored by sjplimp <sjplimp@sandia.gov> on Nov 22 2016, 16:51.

Description

Merge pull request #288 from akohlmey/moltemplate-1.40

update bundled version of moltemplate to v1.40

Details

Committed
GitHub <noreply@github.com>Nov 22 2016, 16:51
Pushed
jungeOct 19 2017, 09:53
Parents
rLAMMPS9e9d9d5aa541: update bundled version of moltemplate to v1.40
rLAMMPSb6f2f0e6e95f: Merge pull request #287 from rbberger/pylammps/docs
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GitHub <noreply@github.com> committed rLAMMPS61e71d23eded: Merge pull request #288 from akohlmey/moltemplate-1.40 (authored by sjplimp <sjplimp@sandia.gov>).Nov 22 2016, 16:51

Merged Changes

CommitAuthorDetailsCommitted
9e9d9d5aa541Axel Kohlmeyer
update bundled version of moltemplate to v1.40 
Nov 21 2016

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Dtools/moltemplate/common
V(dir)tools/moltemplate/{common/amber/ → src/moltemplate_force_fields/amber}
Vtools/moltemplate/{common → src/moltemplate_force_fields}/amber/README.TXT
Vtools/moltemplate/{common → src/moltemplate_force_fields}/amber/amberparm2lt.sh
Vtools/moltemplate/{common → src/moltemplate_force_fields}/amber/amberparm_angle_to_lt.py
Vtools/moltemplate/{common → src/moltemplate_force_fields}/amber/amberparm_bond_to_lt.py
Vtools/moltemplate/{common → src/moltemplate_force_fields}/amber/amberparm_dihedral_to_lt.py
Vtools/moltemplate/{common → src/moltemplate_force_fields}/amber/amberparm_improper_to_lt.py
Vtools/moltemplate/{common → src/moltemplate_force_fields}/amber/amberparm_mass_to_lt.py
Vtools/moltemplate/{common → src/moltemplate_force_fields}/amber/amberparm_pair_to_lt.py
Vtools/moltemplate/{common → src/moltemplate_force_fields}/gaff.lt
Vtools/moltemplate/{common → examples/force_field_explicit_parameters/nanotube+water/moltemplate_files}/graphene.lt
Vtools/moltemplate/{common → examples/force_field_explicit_parameters/nanotube+water/moltemplate_files}/graphite.lt
V(dir)tools/moltemplate/{common/images/ → src/moltemplate_force_fields/images}
Vtools/moltemplate/{common → examples/force_field_explicit_parameters/nanotube+water}/images/graphene_unit_cell.jpg
Vtools/moltemplate/{common → examples/force_field_explicit_parameters/ice_crystal}/images/ice_rect8_unitcell.png
Vtools/moltemplate/{common → src/moltemplate_force_fields}/images/spce_ball_and_stick.jpg
Dtools/moltemplate/common/oplsaa
Vtools/moltemplate/{common/oplsaa → examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator}/AUTHOR.TXT
Vtools/moltemplate/{common → src/moltemplate_force_fields}/oplsaa/README.TXT
Vtools/moltemplate/{common → src/moltemplate_force_fields}/spce.lt
Vtools/moltemplate/{common → examples/force_field_explicit_parameters/ice_crystal/moltemplate_files}/spce_ice_rect16.lt
Vtools/moltemplate/{common → examples/force_field_explicit_parameters/ice_crystal/moltemplate_files}/spce_ice_rect32.lt
Vtools/moltemplate/{common → src/moltemplate_force_fields}/spce_ice_rect8.lt
Vtools/moltemplate/{common → src/moltemplate_force_fields}/tip3p_1983.lt
Vtools/moltemplate/{common → src/moltemplate_force_fields}/tip3p_1983_charmm.lt
Vtools/moltemplate/{common → src/moltemplate_force_fields}/tip3p_2004.lt
Vtools/moltemplate/{common → src/moltemplate_force_fields}/trappe1998.lt
Vtools/moltemplate/{common → src/moltemplate_force_fields}/watmw.lt
Dtools/moltemplate/examples/all_atom_examples
Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/WARNING.TXT
Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene
Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/benzene/README_run.sh
Vtools/moltemplate/examples/{all_atom_examples/force_field_AMBER/benzene → force_field_AMBER/ethylene+benzene}/README_setup.sh
Ptools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_visualize.txt
Deleted after being copied to multiple locations:
tools/moltemplate/examples/force_field_AMBER/benzene/README_visualize.txt
tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt
Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/moltemplate_files
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/benzene/moltemplate_files/benzene.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/benzene/moltemplate_files/system.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/benzene/optional_cleanup/ → force_field_AMBER/benzene/optional_cleanup}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/benzene/optional_cleanup/README_remove_irrelevant_info.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/benzene/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/benzene/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene
Vtools/moltemplate/examples/{all_atom_examples/force_field_AMBER/ethylene+benzene → force_field_OPLSAA/ethylene+benzene_PACKMOL}/README.TXT
Ptools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh
Deleted after being copied to multiple locations:
tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_run.sh
tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_run.sh
tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh
tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_run.sh
tools/moltemplate/examples/force_field_OPLSAA/methane/README_run.sh
tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh
tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_run.sh
Ptools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_setup.sh
Deleted after being copied to multiple locations:
tools/moltemplate/examples/force_field_AMBER/benzene/README_setup.sh
tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh
tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh
tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/ethylene+benzene/images/ → force_field_AMBER/ethylene+benzene/images}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/images/benzene.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/images/ethylene.jpg
Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/moltemplate_files
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA/ → force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA/oplsaa_subset.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/moltemplate_files/ethylene.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/ethylene+benzene/optional_cleanup/ → force_field_AMBER/ethylene+benzene/optional_cleanup}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/optional_cleanup/README_remove_irrelevant_info.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/README_run.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/README_visualize.txt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/WARNING.TXT
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/hexadecane/images/ → force_field_AMBER/hexadecane/images}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/images/hexadecane_LR.jpg
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/hexadecane/moltemplate_files/ → force_field_AMBER/hexadecane/moltemplate_files}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/moltemplate_files/ch2group.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/moltemplate_files/ch3group.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/moltemplate_files/hexadecane.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/moltemplate_files/system.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/hexadecane/optional_cleanup/ → force_field_AMBER/hexadecane/optional_cleanup}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/hexadecane/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/README.TXT
Ptools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh
Deleted after being copied to multiple locations:
tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh
tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_run.sh
Ptools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
Deleted after being copied to multiple locations:
tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
tools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_setup.sh
tools/moltemplate/examples/force_field_OPLSAA/methane/README_setup.sh
tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh
tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/images/ → force_field_AMBER/waterTIP3P+isobutane/images}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/images/isobutane.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/images/water.jpg
Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/isobutane.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/system.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/ → force_field_AMBER/waterTIP3P+isobutane/optional_cleanup}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/waterTIP3P+isobutane/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/WARNING.TXT
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README.TXT
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_run.sh
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/alkane_chain_single/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/alkane_chain_single/images/ → force_field_OPLSAA/alkane_chain_single/images}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/alkane_chain_single/images/ch2_ry90.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/alkane_chain_single/images/ch3_ry60.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/alkane_chain_single/images/t=0.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/alkane_chain_single/images/t=1ns.jpg
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/alkane_chain_single/moltemplate_files/alkane50.lt
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch2group.lt
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch3group.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/ → force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/alkane_chain_single → force_field_OPLSAA/ethylene+benzene}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/alkane_chain_single/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/alkane_chain_single/run.in.min
Ptools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/run.in.nvt
Deleted after being copied to multiple locations:
tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/run.in.nvt
tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/run.in.npt
tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/README.TXT
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_run.sh
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/ethylene+benzene/images/ → force_field_OPLSAA/ethylene+benzene/images}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/images/benzene.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/images/ethylene.jpg
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/ → force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/ethylene+benzene → force_field_OPLSAA/ethylene+benzene_PACKMOL}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/README.TXT
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/ → force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README.TXT
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ → force_field_OPLSAA/ethylene+benzene_PACKMOL/images}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/benzene.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene.jpg
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ → force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/ → force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL → force_field_OPLSAA/hexadecane}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/ → force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.xyz
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/ → force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README.TXT
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_run.sh
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/README_visualize.txt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/WARNING.TXT
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/hexadecane/images/ → force_field_OPLSAA/hexadecane/images}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/ch3group.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/moltemplate_files/hexadecane.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/ → force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/hexadecane → force_field_OPLSAA/methane}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/hexadecane/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane
Vtools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/methane → force_field_OPLSAA/waterSPCE+methane}/README.TXT
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_run.sh
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/methane/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/ → force_field_OPLSAA/methane/moltemplate_files}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/methane/moltemplate_files/methane.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/ → force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/methane → force_field_OPLSAA/waterSPCE+methane}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/methane/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/methane/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/methane/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README.TXT
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPCE+methane/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/ → force_field_OPLSAA/waterSPCE+methane/moltemplate_files}
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/methane.lt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/ → force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/waterSPCE+methane → force_field_OPLSAA/waterSPC_using_OPLSAA}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPCE+methane/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPCE+methane/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPC_using_OPLSAA/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPC_using_OPLSAA/README_visualize.txt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPC_using_OPLSAA/TEST_density_estimate.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/ → force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files}
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/ → force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator}
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/spc.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_explicit
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_explicit/aluminum_crystal_strain/ → force_field_explicit_parameters/aluminum_crystal_strain}
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/aluminum_crystal_strain/README.TXT
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/aluminum_crystal_strain/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit/aluminum_crystal_strain → force_field_OPLSUA_united_atom/propane}/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_explicit/aluminum_crystal_strain/images/ → force_field_explicit_parameters/aluminum_crystal_strain/images}
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/aluminum_crystal_strain/images/AlCell_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_explicit/aluminum_crystal_strain/moltemplate_files/ → force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files}
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/aluminum_crystal_strain/moltemplate_files/README.sh
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/aluminum_crystal_strain/moltemplate_files/al_cell.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/aluminum_crystal_strain/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/aluminum_crystal_strain/run.in
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_explicit/ice_crystal/ → force_field_explicit_parameters/ice_crystal}
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/ice_crystal/README_run.sh
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/ice_crystal/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/ice_crystal/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_explicit/ice_crystal/images/ → force_field_explicit_parameters/ice_crystal/images}
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg
Vtools/moltemplate/{examples/all_atom_examples/force_field_explicit/ice_crystal → src/moltemplate_force_fields}/images/ice_rect8_unitcell.png
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_explicit/ice_crystal/moltemplate_files/ → force_field_explicit_parameters/ice_crystal/moltemplate_files}
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/ice_crystal/moltemplate_files/spce.lt
Vtools/moltemplate/{examples/all_atom_examples/force_field_explicit/ice_crystal/moltemplate_files → src/moltemplate_force_fields}/spce_ice_rect16.lt
Vtools/moltemplate/{examples/all_atom_examples/force_field_explicit/ice_crystal/moltemplate_files → src/moltemplate_force_fields}/spce_ice_rect32.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/ice_crystal/moltemplate_files/spce_ice_rect8.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/ice_crystal/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/ice_crystal/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/ice_crystal/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/README.TXT
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/README_realistic_junctions.txt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/README_run.sh
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_explicit/nanotube+water/images/ → force_field_explicit_parameters/nanotube+water/images}
Vtools/moltemplate/{examples/all_atom_examples/force_field_explicit/nanotube+water → src/moltemplate_force_fields}/images/graphene_unit_cell.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/images/nanotube+walls+water_side_pbc_t=0ps_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/images/nanotube+walls+water_side_pbc_t=108ps_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/images/nanotube+walls+water_side_pbc_t=305ps_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/images/nanotube+walls+water_top_nopbc_t=0_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/images/nanotube+walls_side_nopbc_LR.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/images/water_side_nopbc_LR.jpg
Dtools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/moltemplate_files/README.sh
Vtools/moltemplate/{examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files → src/moltemplate_force_fields}/graphene.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/moltemplate_files/graphene_walls.lt
Vtools/moltemplate/{examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files → src/moltemplate_force_fields}/graphite.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/moltemplate_files/nanotube.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/moltemplate_files/spce.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/moltemplate_files/water_box.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/moltemplate_files/watmw.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit/nanotube+water → coarse_grained_examples/abstract_translocation}/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/nanotube+water/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/README_run.sh
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit/waterSPCE+Na+Cl → force_field_explicit_parameters/aluminum_crystal_strain}/README_visualize.txt
V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/images/ → force_field_explicit_parameters/waterSPCE+Na+Cl/images}
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/images/Cl.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/images/Na.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/images/wat.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg
Dtools/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/moltemplate_files
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/moltemplate_files/ions.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/moltemplate_files/spce.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/moltemplate_files/system.lt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/run.in.npt
Vtools/moltemplate/examples/{all_atom_examples/force_field_explicit → force_field_explicit_parameters}/waterSPCE+Na+Cl/run.in.nvt
Mtools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_setup.sh
Mtools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/system.lt
Vtools/moltemplate/examples/{coarse_grained_examples/abstract_translocation ← all_atom_examples/force_field_explicit/nanotube+water}/run.in.npt
Mtools/moltemplate/examples/coarse_grained_examples/abstract_translocation/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_AMBER/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/WARNING.TXT
A(dir)tools/moltemplate/examples/force_field_AMBER/benzene/
Atools/moltemplate/examples/force_field_AMBER/benzene/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/benzene/README_run.sh
Ptools/moltemplate/examples/force_field_AMBER/benzene/README_setup.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_setup.sh
Ptools/moltemplate/examples/force_field_AMBER/benzene/README_visualize.txt
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_visualize.txt
A(dir)tools/moltemplate/examples/force_field_AMBER/benzene/moltemplate_files/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/benzene/moltemplate_files/benzene.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/benzene/moltemplate_files/system.lt
V(dir)tools/moltemplate/examples/{force_field_AMBER/benzene/optional_cleanup/ ← all_atom_examples/force_field_AMBER/benzene/optional_cleanup}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/benzene/optional_cleanup/README_remove_irrelevant_info.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/benzene/run.in.npt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/benzene/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/
Atools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README.TXT
Ptools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_run.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh
Vtools/moltemplate/examples/{force_field_AMBER/ethylene+benzene ← all_atom_examples/force_field_AMBER/benzene}/README_setup.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_AMBER/ethylene+benzene/images/ ← all_atom_examples/force_field_AMBER/ethylene+benzene/images}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/images/benzene.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/images/ethylene.jpg
A(dir)tools/moltemplate/examples/force_field_AMBER/ethylene+benzene/moltemplate_files/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt
V(dir)tools/moltemplate/examples/{force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA/ ← all_atom_examples/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA/oplsaa_subset.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/moltemplate_files/ethylene.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt
V(dir)tools/moltemplate/examples/{force_field_AMBER/ethylene+benzene/optional_cleanup/ ← all_atom_examples/force_field_AMBER/ethylene+benzene/optional_cleanup}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/optional_cleanup/README_remove_irrelevant_info.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/run.in.npt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_AMBER/hexadecane/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/README_run.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/README_setup.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/README_visualize.txt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/WARNING.TXT
V(dir)tools/moltemplate/examples/{force_field_AMBER/hexadecane/images/ ← all_atom_examples/force_field_AMBER/hexadecane/images}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/images/hexadecane_LR.jpg
V(dir)tools/moltemplate/examples/{force_field_AMBER/hexadecane/moltemplate_files/ ← all_atom_examples/force_field_AMBER/hexadecane/moltemplate_files}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/moltemplate_files/ch2group.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/moltemplate_files/ch3group.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/moltemplate_files/hexadecane.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/moltemplate_files/system.lt
V(dir)tools/moltemplate/examples/{force_field_AMBER/hexadecane/optional_cleanup/ ← all_atom_examples/force_field_AMBER/hexadecane/optional_cleanup}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/run.in.npt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/hexadecane/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/README.TXT
Ptools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh
Ptools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_AMBER/waterTIP3P+isobutane/images/ ← all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/images}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/images/isobutane.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/images/water.jpg
A(dir)tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/isobutane.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/system.lt
V(dir)tools/moltemplate/examples/{force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/ ← all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/run.in.npt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/waterTIP3P+isobutane/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_OPLSAA/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/WARNING.TXT
A(dir)tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/
Atools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README.TXT
Vtools/moltemplate/examples/{force_field_OPLSAA/alkane_chain_single ← all_atom_examples/force_field_AMBER/waterTIP3P+isobutane}/README_run.sh
Ptools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_setup.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/alkane_chain_single/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/alkane_chain_single/images/ ← all_atom_examples/force_field_OPLSAA/alkane_chain_single/images}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/alkane_chain_single/images/ch2_ry90.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/alkane_chain_single/images/ch3_ry60.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/alkane_chain_single/images/t=0.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/alkane_chain_single/images/t=1ns.jpg
A(dir)tools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/alkane_chain_single/moltemplate_files/alkane50.lt
Atools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch2group.lt
Atools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch3group.lt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/ ← all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/{examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator ← common/oplsaa}/AUTHOR.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/alkane_chain_single/moltemplate_files/system.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/alkane_chain_single/run.in.min
Ptools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/run.in.nvt
Copied from tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/README.TXT
Ptools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_run.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh
Ptools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_setup.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene/images/ ← all_atom_examples/force_field_OPLSAA/ethylene+benzene/images}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/images/benzene.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/images/ethylene.jpg
A(dir)tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/ ← all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene ← all_atom_examples/force_field_OPLSAA/alkane_chain_single}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/README.TXT
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/ ← all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/run.in.npt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/
Vtools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene_PACKMOL ← all_atom_examples/force_field_AMBER/ethylene+benzene}/README.TXT
Ptools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh
Vtools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene_PACKMOL ← all_atom_examples/force_field_AMBER/ethylene+benzene}/README_setup.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ ← all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/benzene.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene.jpg
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ ← all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/ ← all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene_PACKMOL ← all_atom_examples/force_field_OPLSAA/ethylene+benzene}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/ ← all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.xyz
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/ ← all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_OPLSAA/hexadecane/
Atools/moltemplate/examples/force_field_OPLSAA/hexadecane/README.TXT
Ptools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_run.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh
Ptools/moltemplate/examples/force_field_OPLSAA/hexadecane/README_setup.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/README_visualize.txt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/WARNING.TXT
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/hexadecane/images/ ← all_atom_examples/force_field_OPLSAA/hexadecane/images}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg
A(dir)tools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/
Atools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt
Atools/moltemplate/examples/force_field_OPLSAA/hexadecane/moltemplate_files/ch3group.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/moltemplate_files/hexadecane.lt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/ ← all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{force_field_OPLSAA/hexadecane ← all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/moltemplate_files/system.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/run.in.npt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/hexadecane/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_OPLSAA/methane/
Atools/moltemplate/examples/force_field_OPLSAA/methane/README.TXT
Ptools/moltemplate/examples/force_field_OPLSAA/methane/README_run.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh
Ptools/moltemplate/examples/force_field_OPLSAA/methane/README_setup.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/methane/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/methane/moltemplate_files/ ← all_atom_examples/force_field_OPLSAA/methane/moltemplate_files}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/methane/moltemplate_files/methane.lt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/ ← all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{force_field_OPLSAA/methane ← all_atom_examples/force_field_OPLSAA/hexadecane}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/methane/moltemplate_files/system.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/methane/run.in.npt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/methane/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/
Vtools/moltemplate/examples/{force_field_OPLSAA/waterSPCE+methane ← all_atom_examples/force_field_OPLSAA/methane}/README.TXT
Ptools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh
Ptools/moltemplate/examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPCE+methane/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/waterSPCE+methane/moltemplate_files/ ← all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files}
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/methane.lt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/ ← all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{force_field_OPLSAA/waterSPCE+methane ← all_atom_examples/force_field_OPLSAA/methane}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/system.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPCE+methane/run.in.npt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPCE+methane/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_OPLSAA/waterSPC_using_OPLSAA/
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPC_using_OPLSAA/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh
Vtools/moltemplate/examples/{force_field_OPLSAA/waterSPC_using_OPLSAA ← all_atom_examples/force_field_AMBER/waterTIP3P+isobutane}/README_setup.sh
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPC_using_OPLSAA/README_visualize.txt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPC_using_OPLSAA/TEST_density_estimate.txt
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/ ← all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files}
V(dir)tools/moltemplate/examples/{force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/ ← all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator}
Vtools/moltemplate/examples/{force_field_OPLSAA/waterSPC_using_OPLSAA ← all_atom_examples/force_field_OPLSAA/waterSPCE+methane}/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/README.TXT
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/spc.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/system.lt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.npt
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_OPLSUA_united_atom/
A(dir)tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/
Atools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README.TXT
Vtools/moltemplate/examples/{force_field_OPLSUA_united_atom/propane ← all_atom_examples/force_field_AMBER/ethylene+benzene}/README_run.sh
Atools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/README_setup.sh
Vtools/moltemplate/examples/{force_field_OPLSUA_united_atom/propane ← all_atom_examples/force_field_explicit/aluminum_crystal_strain}/README_visualize.txt
A(dir)tools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/moltemplate_files/
Atools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/moltemplate_files/propane.lt
Atools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/moltemplate_files/system.lt
Ptools/moltemplate/examples/force_field_OPLSUA_united_atom/propane/run.in.npt
Copied from tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/run.in.nvt
Vtools/moltemplate/examples/{force_field_OPLSUA_united_atom/propane ← all_atom_examples/force_field_OPLSAA/alkane_chain_single}/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_explicit_parameters/
V(dir)tools/moltemplate/examples/{force_field_explicit_parameters/aluminum_crystal_strain/ ← all_atom_examples/force_field_explicit/aluminum_crystal_strain}
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/aluminum_crystal_strain/README.TXT
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/aluminum_crystal_strain/README_setup.sh
Vtools/moltemplate/examples/{force_field_explicit_parameters/aluminum_crystal_strain ← all_atom_examples/force_field_explicit/waterSPCE+Na+Cl}/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_explicit_parameters/aluminum_crystal_strain/images/ ← all_atom_examples/force_field_explicit/aluminum_crystal_strain/images}
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/aluminum_crystal_strain/images/AlCell_LR.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg
V(dir)tools/moltemplate/examples/{force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/ ← all_atom_examples/force_field_explicit/aluminum_crystal_strain/moltemplate_files}
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/aluminum_crystal_strain/moltemplate_files/README.sh
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/aluminum_crystal_strain/moltemplate_files/al_cell.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/aluminum_crystal_strain/moltemplate_files/system.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/aluminum_crystal_strain/run.in
V(dir)tools/moltemplate/examples/{force_field_explicit_parameters/ice_crystal/ ← all_atom_examples/force_field_explicit/ice_crystal}
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/ice_crystal/README_run.sh
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/ice_crystal/README_setup.sh
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/ice_crystal/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_explicit_parameters/ice_crystal/images/ ← all_atom_examples/force_field_explicit/ice_crystal/images}
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg
Vtools/moltemplate/{examples/force_field_explicit_parameters/ice_crystal ← common}/images/ice_rect8_unitcell.png
V(dir)tools/moltemplate/examples/{force_field_explicit_parameters/ice_crystal/moltemplate_files/ ← all_atom_examples/force_field_explicit/ice_crystal/moltemplate_files}
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/ice_crystal/moltemplate_files/spce.lt
Vtools/moltemplate/{examples/force_field_explicit_parameters/ice_crystal/moltemplate_files ← common}/spce_ice_rect16.lt
Vtools/moltemplate/{examples/force_field_explicit_parameters/ice_crystal/moltemplate_files ← common}/spce_ice_rect32.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/ice_crystal/moltemplate_files/spce_ice_rect8.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/ice_crystal/moltemplate_files/system.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/ice_crystal/run.in.npt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/ice_crystal/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/README.TXT
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/README_realistic_junctions.txt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/README_run.sh
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/README_setup.sh
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_explicit_parameters/nanotube+water/images/ ← all_atom_examples/force_field_explicit/nanotube+water/images}
Vtools/moltemplate/{examples/force_field_explicit_parameters/nanotube+water ← common}/images/graphene_unit_cell.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/images/nanotube+walls+water_side_pbc_t=0ps_LR.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/images/nanotube+walls+water_side_pbc_t=108ps_LR.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/images/nanotube+walls+water_side_pbc_t=305ps_LR.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/images/nanotube+walls+water_top_nopbc_t=0_LR.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/images/nanotube+walls_side_nopbc_LR.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/images/water_side_nopbc_LR.jpg
A(dir)tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/moltemplate_files/README.sh
Vtools/moltemplate/{examples/force_field_explicit_parameters/nanotube+water/moltemplate_files ← common}/graphene.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/moltemplate_files/graphene_walls.lt
Vtools/moltemplate/{examples/force_field_explicit_parameters/nanotube+water/moltemplate_files ← common}/graphite.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/moltemplate_files/nanotube.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/moltemplate_files/spce.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/moltemplate_files/system.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/moltemplate_files/water_box.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/moltemplate_files/watmw.lt
Atools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/run.in.npt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/nanotube+water/run.in.nvt
A(dir)tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/README_run.sh
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/README_setup.sh
Vtools/moltemplate/examples/{force_field_explicit_parameters/waterSPCE+Na+Cl ← all_atom_examples/force_field_AMBER/benzene}/README_visualize.txt
V(dir)tools/moltemplate/examples/{force_field_explicit_parameters/waterSPCE+Na+Cl/images/ ← all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/images}
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/images/Cl.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/images/Na.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/images/wat.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg
A(dir)tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/moltemplate_files/ions.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/moltemplate_files/spce.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/moltemplate_files/system.lt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/run.in.npt
Vtools/moltemplate/examples/{force_field_explicit_parameters ← all_atom_examples/force_field_explicit}/waterSPCE+Na+Cl/run.in.nvt
Mtools/moltemplate/moltemplate_manual.pdf
Ptools/moltemplate/src/bonds_by_type.py
Copied to tools/moltemplate/src/chargepairs_by_type.py
Ptools/moltemplate/src/chargepairs_by_type.py
Copied from tools/moltemplate/src/bonds_by_type.py
V(dir)tools/moltemplate/src/{docs_useful_scripts/ → moltemplate_docs_useful_scripts}
Vtools/moltemplate/src/{docs_useful_scripts → moltemplate_docs_useful_scripts}/docs_dump2data.txt
Vtools/moltemplate/src/{docs_useful_scripts → moltemplate_docs_useful_scripts}/docs_extract_lammps_data.txt
Vtools/moltemplate/src/{docs_useful_scripts → moltemplate_docs_useful_scripts}/docs_raw2data.txt
Mtools/moltemplate/src/dump2data.py
Mtools/moltemplate/src/extract_lammps_data.py
Mtools/moltemplate/src/ltemplify.py
Mtools/moltemplate/src/lttree.py
Mtools/moltemplate/src/lttree_check.py
Mtools/moltemplate/src/lttree_postprocess.py
Mtools/moltemplate/src/moltemplate.sh
V(dir)tools/moltemplate/src/{moltemplate_docs_useful_scripts/ ← docs_useful_scripts}
Vtools/moltemplate/src/{moltemplate_docs_useful_scripts ← docs_useful_scripts}/docs_dump2data.txt
Vtools/moltemplate/src/{moltemplate_docs_useful_scripts ← docs_useful_scripts}/docs_extract_lammps_data.txt
Vtools/moltemplate/src/{moltemplate_docs_useful_scripts ← docs_useful_scripts}/docs_raw2data.txt
A(dir)tools/moltemplate/src/moltemplate_force_fields/
V(dir)tools/moltemplate/{src/moltemplate_force_fields/amber/ ← common/amber}
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/amber/README.TXT
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/amber/amberparm2lt.sh
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/amber/amberparm_angle_to_lt.py
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/amber/amberparm_bond_to_lt.py
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/amber/amberparm_dihedral_to_lt.py
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/amber/amberparm_improper_to_lt.py
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/amber/amberparm_mass_to_lt.py
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/amber/amberparm_pair_to_lt.py
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/gaff.lt
Vtools/moltemplate/{src/moltemplate_force_fields ← examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files}/graphene.lt
Vtools/moltemplate/{src/moltemplate_force_fields ← examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files}/graphite.lt
V(dir)tools/moltemplate/{src/moltemplate_force_fields/images/ ← common/images}
Vtools/moltemplate/{src/moltemplate_force_fields ← examples/all_atom_examples/force_field_explicit/nanotube+water}/images/graphene_unit_cell.jpg
Vtools/moltemplate/{src/moltemplate_force_fields ← examples/all_atom_examples/force_field_explicit/ice_crystal}/images/ice_rect8_unitcell.png
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/images/spce_ball_and_stick.jpg
Atools/moltemplate/src/moltemplate_force_fields/loplsaa.lt
A(dir)tools/moltemplate/src/moltemplate_force_fields/oplsaa/
Atools/moltemplate/src/moltemplate_force_fields/oplsaa.lt
Atools/moltemplate/src/moltemplate_force_fields/oplsaa/AUTHOR.TXT
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/oplsaa/README.TXT
Atools/moltemplate/src/moltemplate_force_fields/oplsaa/loplsaa_ext.prm
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/spce.lt
Vtools/moltemplate/{src/moltemplate_force_fields ← examples/all_atom_examples/force_field_explicit/ice_crystal/moltemplate_files}/spce_ice_rect16.lt
Vtools/moltemplate/{src/moltemplate_force_fields ← examples/all_atom_examples/force_field_explicit/ice_crystal/moltemplate_files}/spce_ice_rect32.lt
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/spce_ice_rect8.lt
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/tip3p_1983.lt
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/tip3p_1983_charmm.lt
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/tip3p_2004.lt
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/trappe1998.lt
Vtools/moltemplate/{src/moltemplate_force_fields ← common}/watmw.lt
A(dir)tools/moltemplate/src/moltemplate_scripts_depreciated/
Vtools/moltemplate/src/{moltemplate_scripts_depreciated ← }/oplsaa_moltemplate.py
Mtools/moltemplate/src/nbody_by_type.py
Mtools/moltemplate/src/nbody_by_type_lib.py
Mtools/moltemplate/src/nbody_fix_ttree_assignments.py
Mtools/moltemplate/src/nbody_graph_search.py
Mtools/moltemplate/src/nbody_reorder_atoms.py
Vtools/moltemplate/src/{ → moltemplate_scripts_depreciated}/oplsaa_moltemplate.py
Mtools/moltemplate/src/pdbsort.py
Mtools/moltemplate/src/postprocess_input_script.py
Mtools/moltemplate/src/raw2data.py
Mtools/moltemplate/src/remove_duplicate_atoms.py
Mtools/moltemplate/src/remove_duplicates_nbody.py
Mtools/moltemplate/src/renumber_DATA_first_column.py
Atools/moltemplate/src/tinkerparm2lt.py
Mtools/moltemplate/src/ttree.py
Mtools/moltemplate/src/ttree_lex.py
Mtools/moltemplate/src/ttree_render.py

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_realistic_junctions.txt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_run.sh

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_setup.sh

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/README_visualize.txt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/images/graphene_unit_cell.jpg

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_side_pbc_t=0ps_LR.jpg

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/README.sh

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene.lt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene_walls.lt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphite.lt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/nanotube.lt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/system.lt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/water_box.lt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/moltemplate_files/watmw.lt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/run.in.npt

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tools/moltemplate/examples/force_field_explicit_parameters/nanotube+water/run.in.nvt

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tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_run.sh

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tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_setup.sh

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tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt

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tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/images/Cl.jpg

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tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt

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tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt

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tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt

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tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.npt

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tools/moltemplate/examples/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.nvt

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tools/moltemplate/moltemplate_manual.pdf

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tools/moltemplate/src/bonds_by_type.py

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tools/moltemplate/src/chargepairs_by_type.py

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tools/moltemplate/src/docs_useful_scripts/docs_dump2data.txt

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tools/moltemplate/src/docs_useful_scripts/docs_extract_lammps_data.txt

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tools/moltemplate/src/docs_useful_scripts/docs_raw2data.txt

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tools/moltemplate/src/dump2data.py

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tools/moltemplate/src/extract_lammps_data.py

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tools/moltemplate/src/ltemplify.py

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tools/moltemplate/src/lttree.py

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tools/moltemplate/src/lttree_check.py

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tools/moltemplate/src/moltemplate.sh

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tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_dump2data.txt

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tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_extract_lammps_data.txt

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tools/moltemplate/src/moltemplate_docs_useful_scripts/docs_raw2data.txt

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tools/moltemplate/src/moltemplate_force_fields/amber/README.TXT

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tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh

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tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_angle_to_lt.py

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tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_bond_to_lt.py

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tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_dihedral_to_lt.py

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tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_improper_to_lt.py

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tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_mass_to_lt.py

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tools/moltemplate/src/moltemplate_force_fields/amber/amberparm_pair_to_lt.py

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tools/moltemplate/src/moltemplate_force_fields/gaff.lt

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tools/moltemplate/src/moltemplate_force_fields/graphene.lt

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tools/moltemplate/src/moltemplate_force_fields/loplsaa.lt

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tools/moltemplate/src/moltemplate_force_fields/oplsaa.lt

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tools/moltemplate/src/moltemplate_force_fields/oplsaa/AUTHOR.TXT

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tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT

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tools/moltemplate/src/moltemplate_force_fields/oplsaa/loplsaa_ext.prm

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tools/moltemplate/src/moltemplate_force_fields/spce.lt

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tools/moltemplate/src/moltemplate_force_fields/tip3p_1983.lt

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tools/moltemplate/src/moltemplate_force_fields/tip3p_1983_charmm.lt

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tools/moltemplate/src/moltemplate_force_fields/tip3p_2004.lt

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tools/moltemplate/src/moltemplate_force_fields/trappe1998.lt

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tools/moltemplate/src/moltemplate_force_fields/watmw.lt

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tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py

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tools/moltemplate/src/nbody_by_type.py

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tools/moltemplate/src/nbody_by_type_lib.py

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tools/moltemplate/src/nbody_fix_ttree_assignments.py

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tools/moltemplate/src/nbody_graph_search.py

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tools/moltemplate/src/nbody_reorder_atoms.py

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tools/moltemplate/src/oplsaa_moltemplate.py

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tools/moltemplate/src/pdbsort.py

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tools/moltemplate/src/postprocess_input_script.py

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tools/moltemplate/src/raw2data.py

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tools/moltemplate/src/remove_duplicate_atoms.py

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tools/moltemplate/src/remove_duplicates_nbody.py

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tools/moltemplate/src/renumber_DATA_first_column.py

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tools/moltemplate/src/tinkerparm2lt.py

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tools/moltemplate/src/ttree.py

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tools/moltemplate/src/ttree_lex.py

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tools/moltemplate/src/ttree_render.py

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