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Diffusion lammps 3f68d370b505

Merge branch 'master' into USER-DPD_kokkos: up to date to 30Nov16 patch
3f68d370b505
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Authored by Tim Mattox <timothy.mattox@engilitycorp.com> on Nov 30 2016, 22:57.

Description

Merge branch 'master' into USER-DPD_kokkos: up to date to 30Nov16 patch

Details

Committed
Tim Mattox <timothy.mattox@engilitycorp.com>Nov 30 2016, 22:57
Pushed
jungeOct 19 2017, 09:53
Parents
rLAMMPS6e6776f39635: Finish moving/integrating atom_vec_dpd_kokkos into the Kokkos package
rLAMMPSfb3f597f411c: 30Nov16 patch
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Tim Mattox <timothy.mattox@engilitycorp.com> committed rLAMMPS3f68d370b505: Merge branch 'master' into USER-DPD_kokkos: up to date to 30Nov16 patch (authored by Tim Mattox <timothy.mattox@engilitycorp.com>).Nov 30 2016, 22:57

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.
CommitAuthorDetailsCommitted
fb3f597f411cSteve Plimpton
30Nov16 patch 
Nov 30 2016
d14814ae2efesjplimp/GitHub
Merge pull request #289 from akohlmey/collected-updates-and-bugfixes 
Nov 30 2016
beb5a30f6750Steve Plimpton
new compute global/atom command, also bug fix for descending dump sorts 
Nov 30 2016
7ddb6670c02aAxel Kohlmeyer
fix typo 
Nov 30 2016
789e62388f44Axel Kohlmeyer
simplify code 
Nov 29 2016
7d098bff90d4Jakub Krajniak/Axel Kohlmeyer
update format 
Nov 29 2016
1d970d3cdf50Jakub Krajniak/Axel Kohlmeyer
dihedral_nharmonic: added writing coefficient by write_data 
Nov 29 2016
42d430168b8aAxel Kohlmeyer
fix typo in compute cluster/atom docs 
Nov 29 2016
5ff5bc2a6ce2Axel Kohlmeyer
avoid issues detected by coverity scan 
Nov 29 2016
02ae2d218af5Axel Kohlmeyer
correct broken link to USER-SMD docs PDF 
Nov 28 2016
470908fc939dAxel Kohlmeyer
explicitly disallow dynamic groups with compute rdf 
Nov 24 2016
6759630c1680Steve Plimpton
bug fix for dump sort in descending order 
Nov 24 2016
87781771baf8Axel Kohlmeyer
fix typo and USER-OMP support omission 
Nov 23 2016
df46b9aa38fcAxel Kohlmeyer
rename compute pressure/grem to compute PRESSURE/GREM 
Nov 22 2016
647c6f00ce2bAxel Kohlmeyer
Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into… 
Nov 22 2016
237307eda238dstelter92
small typo and changes 
Nov 22 2016
d58dd4f15989dstelter92
bugfix when parsing mpirun 
Nov 22 2016
ae70f1090f18dstelter92
added readme for grem examples 
Nov 22 2016
59d100ab57f6Steve Plimpton
final prep for 22Nov patch 
Nov 22 2016
61e71d23ededsjplimp/GitHub
Merge pull request #288 from akohlmey/moltemplate-1.40 
Nov 22 2016
b6f2f0e6e95fsjplimp/GitHub
Merge pull request #287 from rbberger/pylammps/docs 
Nov 22 2016
ff0441ac164esjplimp/GitHub
Merge pull request #286 from akohlmey/small-fixes-and-updates 
Nov 22 2016
41907d3110desjplimp/GitHub
Merge pull request #285 from akohlmey/fix-ipi-update 
Nov 22 2016
b95f255af4d4Steve Plimpton
small changes to temper/grem commands 
Nov 22 2016
d7b542101ae8sjplimp/GitHub
Merge pull request #283 from akohlmey/grem-feature 
Nov 22 2016
0ffa50f8e87aSteve Plimpton
tweaked author syntax 
Nov 22 2016
78932159642fAxel Kohlmeyer
small comment/whitespace tweak 
Nov 21 2016
3dff9f20184edstelter92
removed extra file 
Nov 21 2016
dab232c542c1dstelter92
modified temper_grem name to fit conventions, re-ran example to match 
Nov 21 2016
9e9d9d5aa541Axel Kohlmeyer
update bundled version of moltemplate to v1.40 
Nov 21 2016
c982b174a236Axel Kohlmeyer/GitHub
Merge pull request #49 from epfl-cosmo/fix-ipi 
Nov 20 2016
87a5a35bad56Michele Ceriotti
A tiny bugfix for the reset flag, and a brief explanation of the changes 
Nov 20 2016
fd174ce2b1bcMichele Ceriotti
Merge branch 'fix-ipi-update' of https://github.com/akohlmey/lammps into fix-ipi 
Nov 20 2016
b11f376a4f89Michele Ceriotti
Merge branch 'master' of github.com:lammps/lammps 
Nov 19 2016
230b29eae652Axel Kohlmeyer
correct accelerator flags for dpd styles in pair style overview 
Nov 19 2016
2383c31f1565Richard Berger
Created PyLammps documentation 
Nov 19 2016
e175a18bdbd0Axel Kohlmeyer
be more thorough in initializing optional data in pair style dpd/fdt/energy 
Nov 18 2016
a5bde82e3759Axel Kohlmeyer
update .gitignore for recent addition 
Nov 18 2016
d787afcca964Axel Kohlmeyer
also remove generated html files with 'make clean' in docs folder 
Nov 18 2016
176cde8ed32bAxel Kohlmeyer
minor cleanups 
Nov 18 2016
2862c2081501Axel Kohlmeyer
Merge branch 'master' into grem-feature 
Nov 18 2016
78e018829fd2Axel Kohlmeyer
Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into grem… 
Nov 18 2016
c78914e7b334Axel Kohlmeyer
update for fix ipi from michele ceriotti 
Nov 18 2016
635f3ce128ecAxel Kohlmeyer
synchronize USER-SMD examples with code 
Nov 18 2016
81f68e06fde9Axel Kohlmeyer
Merge branch 'master' into doc-updates 
Nov 18 2016
2a026c9ad8eadstelter92
revised temper_grem example, better file management 
Nov 17 2016
4a3091f844efdstelter92
modified temper_grem example with more exchanges 
Nov 17 2016
747c95c52528dstelter92
revised documentation, added temper_grem ref to fix_grem 
Nov 17 2016
5c64934bc812dstelter92
added documention, re-ran temper_grem example 
Nov 17 2016
4e62e58d291dAxel Kohlmeyer/GitHub
Merge pull request #47 from dstelter92/grem-feature 
Nov 17 2016

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Mdoc/Makefile
Adoc/src/Eqs/fix_grem.jpg
Adoc/src/Eqs/fix_grem.tex
Adoc/src/JPG/pylammps_dihedral.jpg
Adoc/src/JPG/pylammps_mc_disordered.jpg
Adoc/src/JPG/pylammps_mc_energies_plot.jpg
Adoc/src/JPG/pylammps_mc_minimum.jpg
Mdoc/src/Manual.txt
Mdoc/src/Section_commands.txt
Mdoc/src/Section_python.txt
Mdoc/src/compute_chunk_atom.txt
Mdoc/src/compute_cluster_atom.txt
Adoc/src/compute_global_atom.txt
Mdoc/src/compute_smd_contact_radius.txt
Mdoc/src/compute_smd_damage.txt
Mdoc/src/compute_smd_hourglass_error.txt
Mdoc/src/compute_smd_internal_energy.txt
Mdoc/src/compute_smd_plastic_strain.txt
Mdoc/src/compute_smd_plastic_strain_rate.txt
Mdoc/src/compute_smd_rho.txt
Mdoc/src/compute_smd_tlsph_defgrad.txt
Mdoc/src/compute_smd_tlsph_dt.txt
Mdoc/src/compute_smd_tlsph_num_neighs.txt
Mdoc/src/compute_smd_tlsph_shape.txt
Mdoc/src/compute_smd_tlsph_strain.txt
Mdoc/src/compute_smd_tlsph_strain_rate.txt
Mdoc/src/compute_smd_tlsph_stress.txt
Mdoc/src/compute_smd_triangle_mesh_vertices.txt
Mdoc/src/compute_smd_ulsph_num_neighs.txt
Mdoc/src/compute_smd_ulsph_strain.txt
Mdoc/src/compute_smd_ulsph_strain_rate.txt
Mdoc/src/compute_smd_ulsph_stress.txt
Mdoc/src/compute_smd_vol.txt
Adoc/src/fix_grem.txt
Mdoc/src/fix_ipi.txt
Mdoc/src/fix_smd_adjust_dt.txt
Mdoc/src/fix_smd_integrate_tlsph.txt
Mdoc/src/fix_smd_integrate_ulsph.txt
Mdoc/src/fix_smd_move_triangulated_surface.txt
Mdoc/src/fix_smd_wall_surface.txt
Mdoc/src/fixes.txt
Mdoc/src/lammps.book
Mdoc/src/pair_smd_tlsph.txt
Mdoc/src/pair_smd_ulsph.txt
Adoc/src/temper_grem.txt
Adoc/src/tutorial_pylammps.txt
Mdoc/src/tutorials.txt
A(dir)examples/USER/misc/grem/
Aexamples/USER/misc/grem/README
A(dir)examples/USER/misc/grem/lj-6rep/
A(dir)examples/USER/misc/grem/lj-6rep/400/
Aexamples/USER/misc/grem/lj-6rep/400/restart.init
A(dir)examples/USER/misc/grem/lj-6rep/405/
Aexamples/USER/misc/grem/lj-6rep/405/restart.init
A(dir)examples/USER/misc/grem/lj-6rep/410/
Aexamples/USER/misc/grem/lj-6rep/410/restart.init
A(dir)examples/USER/misc/grem/lj-6rep/415/
Aexamples/USER/misc/grem/lj-6rep/415/restart.init
A(dir)examples/USER/misc/grem/lj-6rep/420/
Aexamples/USER/misc/grem/lj-6rep/420/restart.init
A(dir)examples/USER/misc/grem/lj-6rep/425/
Aexamples/USER/misc/grem/lj-6rep/425/restart.init
Aexamples/USER/misc/grem/lj-6rep/clean.sh
Aexamples/USER/misc/grem/lj-6rep/double-re-short.py
Aexamples/USER/misc/grem/lj-6rep/in.gREM
Aexamples/USER/misc/grem/lj-6rep/run.sh
Aexamples/USER/misc/grem/lj-6rep/walker.bkp
A(dir)examples/USER/misc/grem/lj-single/
Aexamples/USER/misc/grem/lj-single/in.gREM-npt
Aexamples/USER/misc/grem/lj-single/in.gREM-nvt
Aexamples/USER/misc/grem/lj-single/lj.data
Aexamples/USER/misc/grem/lj-single/log.gREM-npt.9Nov16.g++.1
Aexamples/USER/misc/grem/lj-single/log.gREM-npt.9Nov16.g++.4
Aexamples/USER/misc/grem/lj-single/log.gREM-nvt.9Nov16.g++.1
Aexamples/USER/misc/grem/lj-single/log.gREM-nvt.9Nov16.g++.4
A(dir)examples/USER/misc/grem/lj-temper/
A(dir)examples/USER/misc/grem/lj-temper/0/
Aexamples/USER/misc/grem/lj-temper/0/lj.data
Aexamples/USER/misc/grem/lj-temper/0/log.lammps.0
A(dir)examples/USER/misc/grem/lj-temper/1/
Aexamples/USER/misc/grem/lj-temper/1/lj.data
Aexamples/USER/misc/grem/lj-temper/1/log.lammps.1
A(dir)examples/USER/misc/grem/lj-temper/2/
Aexamples/USER/misc/grem/lj-temper/2/lj.data
Aexamples/USER/misc/grem/lj-temper/2/log.lammps.2
A(dir)examples/USER/misc/grem/lj-temper/3/
Aexamples/USER/misc/grem/lj-temper/3/lj.data
Aexamples/USER/misc/grem/lj-temper/3/log.lammps.3
Aexamples/USER/misc/grem/lj-temper/in.gREM-temper
Mexamples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp
Mexamples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
Mexamples/USER/smd/funnel_flow/funnel_flow.lmp
Mexamples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp
Mexamples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp
Dpython/examples/ipython
Vpython/examples/{ipython → pylammps}/.gitignore
Vpython/examples/{ipython → pylammps}/interface_usage.ipynb
Vpython/examples/{ipython → pylammps}/interface_usage_bonds.ipynb
Vpython/examples/{ipython → pylammps}/simple.ipynb
A(dir)python/examples/pylammps/
Vpython/examples/{pylammps ← ipython}/.gitignore
Apython/examples/pylammps/README
A(dir)python/examples/pylammps/dihedrals/
Apython/examples/pylammps/dihedrals/data.dihedral
Apython/examples/pylammps/dihedrals/dihedral.ipynb
Vpython/examples/{pylammps ← ipython}/interface_usage.ipynb
Vpython/examples/{pylammps ← ipython}/interface_usage_bonds.ipynb
A(dir)python/examples/pylammps/montecarlo/
Apython/examples/pylammps/montecarlo/mc.ipynb
A(dir)python/examples/pylammps/mpi4py/
Apython/examples/pylammps/mpi4py/hello.py
Apython/examples/pylammps/mpi4py/in.melt
Apython/examples/pylammps/mpi4py/melt.py
Vpython/examples/{pylammps ← ipython}/simple.ipynb
Msrc/.gitignore
Msrc/MOLECULE/fix_cmap.cpp
Psrc/REPLICA/temper.cpp
Copied to src/USER-MISC/temper_grem.cpp
Msrc/USER-CG-CMM/angle_sdk.cpp
Msrc/USER-COLVARS/ndx_group.cpp
Msrc/USER-DPD/pair_dpd_fdt_energy.cpp
Msrc/USER-EFF/fix_nh_eff.cpp
Msrc/USER-H5MD/dump_h5md.cpp
Msrc/USER-MISC/README
Asrc/USER-MISC/compute_pressure_grem.cpp
Psrc/USER-MISC/compute_pressure_grem.h
Copied from src/compute_pressure.h
Msrc/USER-MISC/dihedral_nharmonic.cpp
Msrc/USER-MISC/dihedral_nharmonic.h
Asrc/USER-MISC/fix_grem.cpp
Asrc/USER-MISC/fix_grem.h
Msrc/USER-MISC/fix_ipi.cpp
Msrc/USER-MISC/fix_ipi.h
Msrc/USER-MISC/fix_ti_spring.cpp
Msrc/USER-MISC/pair_agni.cpp
Psrc/USER-MISC/temper_grem.cpp
Copied from src/REPLICA/temper.cpp
Asrc/USER-MISC/temper_grem.h
Msrc/USER-OMP/fix_omp.cpp
Msrc/USER-OMP/pppm_disp_omp.cpp
Msrc/USER-OMP/thr_data.cpp
Msrc/USER-OMP/thr_omp.cpp
Msrc/USER-PHONON/fix_phonon.cpp
Msrc/USER-SMD/fix_smd_wall_surface.cpp
Msrc/USER-SMD/pair_smd_hertz.cpp
Msrc/USER-SMD/pair_smd_triangulated_surface.cpp
Msrc/compute.cpp
Msrc/compute_bond_local.cpp
Asrc/compute_global_atom.cpp
Asrc/compute_global_atom.h
Psrc/compute_pressure.h
Copied to src/USER-MISC/compute_pressure_grem.h
Msrc/compute_rdf.cpp
Msrc/dump.cpp
Msrc/finish.cpp
Msrc/fix_ave_time.cpp
Msrc/fix_nh.cpp
Msrc/version.h
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
Vtools/moltemplate/examples/{all_atom_examples/force_field_AMBER/benzene → force_field_OPLSAA/ethylene+benzene_PACKMOL}/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/benzene/README_run.sh
Ptools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_setup.sh
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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
Ptools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_visualize.txt
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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
Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README.TXT
Vtools/moltemplate/examples/{all_atom_examples → }/force_field_AMBER/ethylene+benzene/README_run.sh
Ptools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_setup.sh
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tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
tools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh
tools/moltemplate/examples/force_field_OPLSAA/hexadecane/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
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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
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V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/ethylene+benzene/optional_cleanup/ → force_field_AMBER/ethylene+benzene/optional_cleanup}
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Dtools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane
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V(dir)tools/moltemplate/examples/{all_atom_examples/force_field_AMBER/hexadecane/optional_cleanup/ → force_field_AMBER/hexadecane/optional_cleanup}
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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
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/waterTIP3P+isobutane/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
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
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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
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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
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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
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Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files
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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
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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
Dtools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/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
Vtools/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/waterTIP3P+isobutane/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
Vtools/moltemplate/examples/{ ← all_atom_examples}/force_field_AMBER/ethylene+benzene/README_run.sh
Ptools/moltemplate/examples/force_field_AMBER/ethylene+benzene/README_setup.sh
Copied from tools/moltemplate/examples/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/ethylene+benzene/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
Ptools/moltemplate/examples/force_field_OPLSAA/alkane_chain_single/README_run.sh
Copied from tools/moltemplate/examples/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/waterTIP3P+isobutane/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/waterTIP3P+isobutane/README_run.sh
Vtools/moltemplate/examples/{force_field_OPLSAA/ethylene+benzene ← all_atom_examples/force_field_AMBER/waterTIP3P+isobutane}/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/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/waterTIP3P+isobutane/README_run.sh
Ptools/moltemplate/examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/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_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/waterTIP3P+isobutane/README_run.sh
Vtools/moltemplate/examples/{force_field_OPLSAA/hexadecane ← all_atom_examples/force_field_AMBER/ethylene+benzene}/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/waterTIP3P+isobutane/README_run.sh
Ptools/moltemplate/examples/force_field_OPLSAA/methane/README_setup.sh
Copied from tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/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/{ ← all_atom_examples}/force_field_OPLSAA/waterSPCE+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/waterTIP3P+isobutane/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/benzene/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/benzene}/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/waterTIP3P+isobutane}/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/msi2lmp/frc_files/README

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