ProtoMS documentation

• Introduction
  • Formatting
• Changes and New Features
  • GCAP Simulations
  • Grand Canonical Integration
  • Free Energy Calculations
  • protomslib
  • Restarting Simulations
  • Water Clustering
• Compilation and Installation
  • Programming Language
  • Requirements
  • Installing ProtoMS
  • Customising the Build
  • Using Docker
• Design of ProtoMS
  • Proteins / Solutes / Solvents / GCSolutes
  • Classical forcefields
  • Perturbations
  • Generic Moves
• Executing ProtoMS
  • File output
  • Simulation parameters
  • Specifying input files
  • Running a Simulation
  • Setup and analysis tools
• Input Files
  • Parameter / Forcefield Files
  • Templates
  • Automated Creation of Parameter and Template Files
  • Protein File
  • Solute File
  • GCsolute File
  • Solvent File
  • Restart File
• protoms.py
• Tools
  • ambertools.py
  • build_template.py
  • calc_clusters.py
  • calc_density.py
  • calc_dg.py
  • calc_dg_cycle.py
  • calc_gcap_surface.py
  • calc_gci.py
  • calc_replicapath.py
  • calc_rmsd.py
  • calc_series.py
  • calc_ti_decomposed.py
  • clear_gcmcbox.py
  • convertatomnames.py
  • convertwater.py
  • distribute_waters.py
  • divide_pdb.py
  • generate_input.py
  • make_dummy.py
  • make_gcmcbox.py
  • make_single.py
  • merge_templates.py
  • plot_theta.py
  • scoop.py
  • solvate.py
  • split_jawswater.py
• Test Suite
  • Dependencies
  • Running all tests
  • Individual tests