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Some Python scripts for setting up and analysing MD simulations

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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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