Name		Name	Last commit message	Last commit date
SilicaCharges		SilicaCharges
README.md		README.md
SlipLJ.ipynb		SlipLJ.ipynb
adjust_substrate.py		adjust_substrate.py
amorphous-substrate.ipynb		amorphous-substrate.ipynb
assemble_system.py		assemble_system.py
assemble_system_shift.py		assemble_system_shift.py
assemble_system_vel.py		assemble_system_vel.py
atomtypes.itp		atomtypes.itp
atomtypes_mod.itp		atomtypes_mod.itp
connectivity_free_energy.py		connectivity_free_energy.py
contact_line_dumping.py		contact_line_dumping.py
contact_line_tracing.py		contact_line_tracing.py
create_confined_water_butanol.ipynb		create_confined_water_butanol.ipynb
creation_carve.py		creation_carve.py
creation_carve_2D.py		creation_carve_2D.py
creation_double_layer.py		creation_double_layer.py
creation_droplet.py		creation_droplet.py
creation_h2o.py		creation_h2o.py
creation_sub.py		creation_sub.py
fill_topology.py		fill_topology.py
free-workflow.ipynb		free-workflow.ipynb
free_energy_analysis.py		free_energy_analysis.py
free_energy_analysis_step.py		free_energy_analysis_step.py
free_energy_sub.py		free_energy_sub.py
grafted-silica.ipynb		grafted-silica.ipynb
hydrogen_bonds.py		hydrogen_bonds.py
initialize-deform.ipynb		initialize-deform.ipynb
initialize_linear.py		initialize_linear.py
lambda_dynamics.py		lambda_dynamics.py
lj-posers.itp		lj-posers.itp
lj-substrate.itp		lj-substrate.itp
lj.awk		lj.awk
make_disk.awk		make_disk.awk
md_parameters.py		md_parameters.py
mdconf.py		mdconf.py
mdconf_oop.py		mdconf_oop.py
merge_droplet.py		merge_droplet.py
nano-shear.ipynb		nano-shear.ipynb
noneq_parabolic.py		noneq_parabolic.py
prepare-couette.ipynb		prepare-couette.ipynb
prepare-hamaker.ipynb		prepare-hamaker.ipynb
prepare-poiseuille.ipynb		prepare-poiseuille.ipynb
prepare-reduced.ipynb		prepare-reduced.ipynb
produce_grafted_substrate.py		produce_grafted_substrate.py
quad.awk		quad.awk
quadrupole_analysis.py		quadrupole_analysis.py
quadrupole_compress.py		quadrupole_compress.py
quadrupole_orientation.py		quadrupole_orientation.py
quadrupole_shift.py		quadrupole_shift.py
quadrupole_temperature.py		quadrupole_temperature.py
read_density.py		read_density.py
rescale-posres.ipynb		rescale-posres.ipynb
roughfrac.py		roughfrac.py
shape_substrate.py		shape_substrate.py
shape_system.py		shape_system.py
shift_resize_system.py		shift_resize_system.py
shift_velocity_droplet.py		shift_velocity_droplet.py
silica.itp		silica.itp
silica_mod.itp		silica_mod.itp
surface_tension.py		surface_tension.py
system.mdp		system.mdp
system.top		system.top
system_ref.top		system_ref.top
temperature-profile.ipynb		temperature-profile.ipynb
test-sp-artifact.ipynb		test-sp-artifact.ipynb
test_mdoop.py		test_mdoop.py
test_roughness.py		test_roughness.py
uncertainty-quantification.py		uncertainty-quantification.py
vapour.py		vapour.py
velocity_distribution.py		velocity_distribution.py
wall_location.py		wall_location.py
wat_equil.gro		wat_equil.gro
water-glycerol-nanoconfined.ipynb		water-glycerol-nanoconfined.ipynb
wenzel.py		wenzel.py
workflow_glycerol.ipynb		workflow_glycerol.ipynb
workflow_vapour.ipynb		workflow_vapour.ipynb
xvg_read.py		xvg_read.py
zoom_contact_line.py		zoom_contact_line.py
zoom_nearwall.py		zoom_nearwall.py

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python_for_md

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Some Python scripts for setting up and analysing MD simulations

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