mstk

mstk is a toolkit for preparing, running and analyzing molecular simulations. It simplifies the workflow of setting up a simulation by manageable atom type and force field assignment, topology manipulation, trajectory reading/writing, etc…

• Installation
  • Install dependencies
  • Install mstk
• Examples
  • Assign atom types using customized typing rule
  • Generate input files for simulation engines

Modules

• Topology
  • Topology definition
  • Virtual site
  • Topology parser
• Force field
  • Typing engine
  • Force field definition
  • Force field parser
• Simulation system
  • mstk.simsys.System
  • Exporter
• Trajectory
  • mstk.trajectory.Trajectory
  • mstk.trajectory.Frame
  • Trajectory handler
• OpenMM helper
  • Forces
  • Reporters
  • Parsers
• Solvation Free Energy
  • Lambda Schedule
  • Initial Force Decomposition
  • Final Alchemical Force Table
  • API Reference
• Chemistry
  • mstk.chem.element.Element
  • mstk.chem.formula.Formula
  • mstk.chem.constant
• Job scheduler
  • mstk.scheduler.PbsJob
  • mstk.scheduler.JobParameter
  • mstk.scheduler.Scheduler
  • mstk.scheduler.Slurm
  • mstk.scheduler.RemoteSlurm
• Analyzer
  • Structural analysis
  • Structural analysis for vapor-liquid interface
  • Time series analysis
  • Curve fitting
• Wrappers
  • mstk.wrapper.GMX
  • mstk.wrapper.Gauss
  • mstk.wrapper.Packmol

License

mstk is licensed under LGPL v2.1