├── .gitignore ├── Creating_systems_of_proteins_and_enzymes_in_IL_mixtures.pptx ├── GMX_Scaling_icc17.xlsx ├── GROMACS_CUDA.txt ├── Gromacs2020_plumed_on_Cori.txt ├── LICENSE ├── README.md ├── april2016_jim_gromacscompilecommands.txt ├── boxmaker ├── README.md ├── acpype.py ├── boxmaker.bash ├── boxmaker.inp └── boxmaker.pbs ├── examples ├── IL_density_example_ffmaker_boxmaker │ ├── .ipynb_checkpoints │ │ └── Using ffmaker and boxmaker to calculate density of an Ionic Liquid-checkpoint.ipynb │ ├── BMI.pdb │ ├── BMI_TF2.inp │ ├── GROMACS.pbs │ ├── README.md │ ├── TF2.pdb │ ├── Using ffmaker and boxmaker to calculate density of an Ionic Liquid.ipynb │ ├── acpype.py │ ├── activate_amber14.sh │ ├── boxmaker.bash │ ├── boxmaker.inp │ ├── boxmaker.pbs │ ├── directory.inp │ ├── environment.sh │ ├── ffmaker.bash │ ├── ffmaker.inp │ ├── master.sh │ ├── min.mdp │ ├── nodeseaker.sh │ ├── npt.mdp │ ├── packmol.inp │ ├── salt.inp │ ├── salt.sh │ ├── setup.sh │ ├── spAnalysis.sh │ ├── spFF.sh │ └── spMD.sh └── README.md ├── ffmaker ├── README.md ├── TF2.pdb ├── ffmaker.bash └── ffmaker.inp ├── mdp_files ├── em.mdp ├── npt_equil.mdp ├── npt_prod.mdp ├── nve.mdp ├── nvt_equil.mdp ├── nvt_frozen.mdp └── nvt_heat.mdp ├── scaling ├── scaling_gmx18_mox_ikt.xlsx ├── scalingdata.xlsx └── scalingdata_30Nov2017.xlsx ├── self_assembled_monolayer_builder.sh ├── submission ├── GROMACS18_ikt.sh └── GROMACS18_mox.sh └── track_secondary_structure.sh /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | -------------------------------------------------------------------------------- /Creating_systems_of_proteins_and_enzymes_in_IL_mixtures.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/Creating_systems_of_proteins_and_enzymes_in_IL_mixtures.pptx -------------------------------------------------------------------------------- /GMX_Scaling_icc17.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/GMX_Scaling_icc17.xlsx -------------------------------------------------------------------------------- /GROMACS_CUDA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/GROMACS_CUDA.txt -------------------------------------------------------------------------------- /Gromacs2020_plumed_on_Cori.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/Gromacs2020_plumed_on_Cori.txt -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/README.md -------------------------------------------------------------------------------- /april2016_jim_gromacscompilecommands.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/april2016_jim_gromacscompilecommands.txt -------------------------------------------------------------------------------- /boxmaker/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/boxmaker/README.md -------------------------------------------------------------------------------- /boxmaker/acpype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/boxmaker/acpype.py -------------------------------------------------------------------------------- /boxmaker/boxmaker.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/boxmaker/boxmaker.bash -------------------------------------------------------------------------------- /boxmaker/boxmaker.inp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/boxmaker/boxmaker.inp -------------------------------------------------------------------------------- /boxmaker/boxmaker.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/boxmaker/boxmaker.pbs -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/.ipynb_checkpoints/Using ffmaker and boxmaker to calculate density of an Ionic Liquid-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/.ipynb_checkpoints/Using ffmaker and boxmaker to calculate density of an Ionic Liquid-checkpoint.ipynb -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/BMI.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/BMI.pdb -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/BMI_TF2.inp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/BMI_TF2.inp -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/GROMACS.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/GROMACS.pbs -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/README.md -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/TF2.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/TF2.pdb -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/Using ffmaker and boxmaker to calculate density of an Ionic Liquid.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/Using ffmaker and boxmaker to calculate density of an Ionic Liquid.ipynb -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/acpype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/acpype.py -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/activate_amber14.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/activate_amber14.sh -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/boxmaker.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/boxmaker.bash -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/boxmaker.inp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/boxmaker.inp -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/boxmaker.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/boxmaker.pbs -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/directory.inp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/directory.inp -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/environment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/environment.sh -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/ffmaker.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/ffmaker.bash -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/ffmaker.inp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/ffmaker.inp -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/master.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/master.sh -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/min.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/min.mdp -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/nodeseaker.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/nodeseaker.sh -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/npt.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/npt.mdp -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/packmol.inp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/packmol.inp -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/salt.inp: -------------------------------------------------------------------------------- 1 | BMI,TF2,1.456 2 | -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/salt.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/salt.sh -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/setup.sh -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/spAnalysis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/spAnalysis.sh -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/spFF.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/spFF.sh -------------------------------------------------------------------------------- /examples/IL_density_example_ffmaker_boxmaker/spMD.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/IL_density_example_ffmaker_boxmaker/spMD.sh -------------------------------------------------------------------------------- /examples/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/examples/README.md -------------------------------------------------------------------------------- /ffmaker/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/ffmaker/README.md -------------------------------------------------------------------------------- /ffmaker/TF2.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/ffmaker/TF2.pdb -------------------------------------------------------------------------------- /ffmaker/ffmaker.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/ffmaker/ffmaker.bash -------------------------------------------------------------------------------- /ffmaker/ffmaker.inp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/ffmaker/ffmaker.inp -------------------------------------------------------------------------------- /mdp_files/em.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/mdp_files/em.mdp -------------------------------------------------------------------------------- /mdp_files/npt_equil.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/mdp_files/npt_equil.mdp -------------------------------------------------------------------------------- /mdp_files/npt_prod.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/mdp_files/npt_prod.mdp -------------------------------------------------------------------------------- /mdp_files/nve.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/mdp_files/nve.mdp -------------------------------------------------------------------------------- /mdp_files/nvt_equil.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/mdp_files/nvt_equil.mdp -------------------------------------------------------------------------------- /mdp_files/nvt_frozen.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/mdp_files/nvt_frozen.mdp -------------------------------------------------------------------------------- /mdp_files/nvt_heat.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/mdp_files/nvt_heat.mdp -------------------------------------------------------------------------------- /scaling/scaling_gmx18_mox_ikt.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/scaling/scaling_gmx18_mox_ikt.xlsx -------------------------------------------------------------------------------- /scaling/scalingdata.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/scaling/scalingdata.xlsx -------------------------------------------------------------------------------- /scaling/scalingdata_30Nov2017.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/scaling/scalingdata_30Nov2017.xlsx -------------------------------------------------------------------------------- /self_assembled_monolayer_builder.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/self_assembled_monolayer_builder.sh -------------------------------------------------------------------------------- /submission/GROMACS18_ikt.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/submission/GROMACS18_ikt.sh -------------------------------------------------------------------------------- /submission/GROMACS18_mox.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/submission/GROMACS18_mox.sh -------------------------------------------------------------------------------- /track_secondary_structure.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UWPRG/GROMACS/HEAD/track_secondary_structure.sh --------------------------------------------------------------------------------