« back to all changes in this revision
Viewing changes to examples/ASPHERE/dimer/in.dimer.mp
- Committer: Package Import Robot
- Date: 2015-04-29 23:44:49 UTC
- mfrom: (5.1.3 experimental)
- Revision ID: package-import@ubuntu.com-20150429234449-mbhy9utku6hp6oq8
Upload into unstable.
- files added:
- .pc/10_set_configure_flags.patch
- .pc/10_set_configure_flags.patch/src
- .pc/10_set_configure_flags.patch/src/MAKE
- bench/FERMI
- bench/KEPLER
- examples/MC
- examples/USER/gle
- examples/USER/i-pi
- examples/USER/pimd
- examples/USER/pimd/para-h2
- examples/USER/pimd/prot-hairpin
- examples/USER/quip
- examples/USER/srp
- examples/accelerate
- examples/balance
- examples/coreshell
- examples/qeq
- examples/snap
- examples/streitz
- lib/kim
- lib/kokkos
- lib/kokkos/TPL
- lib/kokkos/TPL/cmake
- lib/kokkos/TPL/cub
- lib/kokkos/TPL/cub/block
- lib/kokkos/TPL/cub/block/specializations
- lib/kokkos/TPL/cub/device
- lib/kokkos/TPL/cub/device/block
- lib/kokkos/TPL/cub/device/block/specializations
- lib/kokkos/TPL/cub/grid
- lib/kokkos/TPL/cub/host
- lib/kokkos/TPL/cub/thread
- lib/kokkos/TPL/cub/warp
- lib/kokkos/TPL/cub/warp/specializations
- lib/kokkos/algorithms
- lib/kokkos/algorithms/src
- lib/kokkos/containers
- lib/kokkos/containers/src
- lib/kokkos/containers/src/impl
- lib/kokkos/core
- lib/kokkos/core/src
- lib/kokkos/core/src/Cuda
- lib/kokkos/core/src/OpenMP
- lib/kokkos/core/src/Qthread
- lib/kokkos/core/src/Threads
- lib/kokkos/core/src/impl
- lib/molfile
- lib/quip
- lib/voronoi
- src/CORESHELL
- src/KOKKOS
- src/MAKE/MACHINES
- src/MAKE/OPTIONS
- src/QEQ
- src/SNAP
- src/USER-INTEL
- src/USER-INTEL/TEST
- src/USER-QUIP
- tools/i-pi
- tools/i-pi/drivers
- tools/i-pi/examples
- tools/i-pi/examples/lammps
- tools/i-pi/examples/lammps/h2o-piglet.2
- tools/i-pi/examples/lammps/h2o-piglet.4
- tools/i-pi/examples/lammps/h2o-piglet.8
- tools/i-pi/examples/lammps/h2o-pimd
- tools/i-pi/examples/lammps/h2o-pimd-rpc
- tools/i-pi/examples/tutorial
- tools/i-pi/examples/tutorial/tutorial-1
- tools/i-pi/examples/tutorial/tutorial-2
- tools/i-pi/examples/tutorial/tutorial-3
- tools/i-pi/ipi
- tools/i-pi/ipi/engine
- tools/i-pi/ipi/inputs
- tools/i-pi/ipi/interfaces
- tools/i-pi/ipi/tests
- tools/i-pi/ipi/utils
- tools/i-pi/ipi/utils/io
- tools/i-pi/licenses
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/optional_cleanup
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_visualize.txt
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/images
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/optional_cleanup
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/images
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/optional_cleanup
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/images
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/images/water.jpg
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/images
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/images/t=1ns.jpg
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/images
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/images/ethylene.jpg
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/minimal_versions
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/images
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/images
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/methane.lt
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator
- tools/moltemplate/examples/all_atom_examples/force_field_explicit
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/aluminum_crystal_strain
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/aluminum_crystal_strain/README.TXT
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/aluminum_crystal_strain/images
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/aluminum_crystal_strain/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/ice_crystal
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/ice_crystal/images
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/ice_crystal/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/images
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/images
- tools/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples
- tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE
- tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_setup.sh
- tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/images
- tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/version_more_comments
- tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples
- tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL
- tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/images
- tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/packmol_files
- tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed
- tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/images
- tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer
- tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_visualize.txt
- tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/images
- tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/images/t=4ns_occ.png
- tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer
- tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/images
- tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/abstract_translocation
- tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/images
- tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/moltemplate_files/walls.lt
- tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013
- tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_FIRST.txt
- tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/images
- tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010
- tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images
- tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/calc_table
- tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff
- tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005
- tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/images
- tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table
- tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/for_visualization
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm
- tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2
- tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010
- tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/images
- tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files
- tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table
- tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff
- tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/packmol_files
- tools/moltemplate/examples/file_conversion_examples
- tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples
- tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt
- tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images
- tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization
- tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt
- tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples
- tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile
- tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files
- tools/moltemplate/examples/misc_examples
- tools/moltemplate/examples/misc_examples/menger_sponge
- tools/moltemplate/examples/misc_examples/menger_sponge/images
- tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files
- tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/elegant_inefficient_version
- tools/moltemplate/examples/misc_examples/pyramids_vs_gravity
- tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/images
- tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/moltemplate_files
- files removed:
- .pc/fix_format_not_a_string.patch
- .pc/fix_format_not_a_string.patch/src
- .pc/set_configure_flags.patch
- .pc/set_configure_flags.patch/src
- .pc/set_configure_flags.patch/src/MAKE
- bench/GPU
- examples/USER/cuda
- examples/gpu
- tools/moltemplate/examples/CG_biomolecules
- tools/moltemplate/examples/CG_biomolecules/membrane+protein
- tools/moltemplate/examples/CG_biomolecules/membrane+protein/images
- tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg
- tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files
- tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table
- tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff
- tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005
- tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images
- tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files
- tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table
- tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff
- tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat
- tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013
- tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images
- tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm
- tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2
- tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010
- tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images
- tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files
- tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table
- tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff
- tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files
- tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DLPC.xyz
- tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DPPC.xyz
- tools/moltemplate/examples/CG_misc
- tools/moltemplate/examples/CG_misc/2bead_heteropolymer
- tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images
- tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization
- tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files
- tools/moltemplate/examples/CG_misc/random_heteropolymer
- tools/moltemplate/examples/CG_misc/random_heteropolymer/images
- tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization
- tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files
- tools/moltemplate/examples/CG_misc/translocation
- tools/moltemplate/examples/CG_misc/translocation/images
- tools/moltemplate/examples/CG_misc/translocation/moltemplate_files
- tools/moltemplate/examples/CG_solvent
- tools/moltemplate/examples/CG_solvent/cyclododecane+watMW
- tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images
- tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization
- tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files
- tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments
- tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples
- tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane
- tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images
- tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/optional_cleanup
- tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane
- tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images
- tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/optional_cleanup
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/images
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator
- tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions
- tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain
- tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images
- tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples
- tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt
- tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT
- tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images
- tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization
- tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/all_atom_examples/hexadecane
- tools/moltemplate/examples/all_atom_examples/hexadecane/images
- tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/ice_crystal
- tools/moltemplate/examples/all_atom_examples/ice_crystal/images
- tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/nanotube+water
- tools/moltemplate/examples/all_atom_examples/nanotube+water/images
- tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization
- tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples
- tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile
- tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files
- tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl
- tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images
- tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization
- tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools
- tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files
- tools/moltemplate/examples/silly
- tools/moltemplate/examples/silly/pyramids_vs_gravity
- tools/moltemplate/examples/silly/pyramids_vs_gravity/images
- tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files
- tools/moltemplate/examples/silly/sierpinski
- tools/moltemplate/examples/silly/sierpinski/images
- tools/moltemplate/examples/silly/sierpinski/moltemplate_files
- tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version
- tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt
- files modified:
- .pc/applied-patches
- tools/moltemplate/src/nbody_by_type_lib.py *
- tools/moltemplate/src/nbody_graph_search.py *
added
removed
examples/ASPHERE/dimer/in.dimer.mp
