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openbiosim - biosimspace
Logo
Branch
  • Features
  • Installation
  • Compatibility
  • Quick Start Guide
  • Tutorials
    • Crystal water
    • Hydration free energy
    • Metadynamics
    • Alchemical Protein Mutations
    • Alchemical Transfer Method
  • Detailed Guides
    • Nodes
    • Protocols
  • API Documentation
    • BioSimSpace.Align
      • BioSimSpace.Align.generateNetwork
      • BioSimSpace.Align.matchAtoms
      • BioSimSpace.Align.rmsdAlign
      • BioSimSpace.Align.flexAlign
      • BioSimSpace.Align.merge
      • BioSimSpace.Align.viewMapping
    • BioSimSpace.Box
      • BioSimSpace.Box.boxTypes
      • BioSimSpace.Box.generateBoxParameters
      • BioSimSpace.Box.cubic
      • BioSimSpace.Box.rhombicDodecahedronSquare
      • BioSimSpace.Box.rhombicDodecahedronHexagon
      • BioSimSpace.Box.truncatedOctahedron
    • BioSimSpace.Convert
      • BioSimSpace.Convert.smiles
      • BioSimSpace.Convert.supportedFormats
      • BioSimSpace.Convert.to
      • BioSimSpace.Convert.toBioSimSpace
      • BioSimSpace.Convert.toOpenMM
      • BioSimSpace.Convert.toRDKit
      • BioSimSpace.Convert.toSire
    • BioSimSpace.FreeEnergy
      • BioSimSpace.FreeEnergy.Relative
      • BioSimSpace.FreeEnergy.ATMSetup
      • BioSimSpace.FreeEnergy.ATM
      • BioSimSpace.FreeEnergy.engines
      • BioSimSpace.FreeEnergy.getData
    • BioSimSpace.Gateway
      • BioSimSpace.Gateway.Node
      • BioSimSpace.Gateway.Boolean
      • BioSimSpace.Gateway.Integer
      • BioSimSpace.Gateway.Float
      • BioSimSpace.Gateway.String
      • BioSimSpace.Gateway.File
      • BioSimSpace.Gateway.FileSet
      • BioSimSpace.Gateway.Length
      • BioSimSpace.Gateway.Area
      • BioSimSpace.Gateway.Volume
      • BioSimSpace.Gateway.Charge
      • BioSimSpace.Gateway.Energy
      • BioSimSpace.Gateway.Pressure
      • BioSimSpace.Gateway.Temperature
      • BioSimSpace.Gateway.Time
    • BioSimSpace.IO
      • BioSimSpace.IO.clearCache
      • BioSimSpace.IO.disableCache
      • BioSimSpace.IO.enableCache
      • BioSimSpace.IO.fileFormats
      • BioSimSpace.IO.formatInfo
      • BioSimSpace.IO.readMolecules
      • BioSimSpace.IO.readPDB
      • BioSimSpace.IO.readPerturbableSystem
      • BioSimSpace.IO.saveMolecules
      • BioSimSpace.IO.savePerturbableSystem
    • BioSimSpace.Metadynamics
      • BioSimSpace.Metadynamics.engines
      • BioSimSpace.Metadynamics.run
      • BioSimSpace.Metadynamics.Bound
      • BioSimSpace.Metadynamics.Grid
      • BioSimSpace.Metadynamics.Restraint
      • BioSimSpace.Metadynamics.CollectiveVariable
        • BioSimSpace.Metadynamics.CollectiveVariable.list
        • BioSimSpace.Metadynamics.CollectiveVariable.makeFunnel
        • BioSimSpace.Metadynamics.CollectiveVariable.viewFunnel
        • BioSimSpace.Metadynamics.CollectiveVariable.Distance
        • BioSimSpace.Metadynamics.CollectiveVariable.Funnel
        • BioSimSpace.Metadynamics.CollectiveVariable.RMSD
        • BioSimSpace.Metadynamics.CollectiveVariable.Torsion
    • BioSimSpace.MD
      • BioSimSpace.MD.engines
      • BioSimSpace.MD.run
    • BioSimSpace.Node
      • BioSimSpace.Node.help
      • BioSimSpace.Node.list
      • BioSimSpace.Node.run
      • BioSimSpace.Node.setNodeDirectory
    • BioSimSpace.Notebook
      • BioSimSpace.Notebook.plot
      • BioSimSpace.Notebook.plotContour
      • BioSimSpace.Notebook.plotOverlapMatrix
      • BioSimSpace.Notebook.View
    • BioSimSpace.Parameters
      • BioSimSpace.Parameters.amberForceFields
      • BioSimSpace.Parameters.amberProteinForceFields
      • BioSimSpace.Parameters.ff03
      • BioSimSpace.Parameters.ff14SB
      • BioSimSpace.Parameters.ff99
      • BioSimSpace.Parameters.ff99SB
      • BioSimSpace.Parameters.ff99SBildn
      • BioSimSpace.Parameters.forceFields
      • BioSimSpace.Parameters.gaff
      • BioSimSpace.Parameters.gaff2
      • BioSimSpace.Parameters.openForceFields
      • BioSimSpace.Parameters.openff_unconstrained_1_0_0
      • BioSimSpace.Parameters.openff_unconstrained_1_0_0_RC1
      • BioSimSpace.Parameters.openff_unconstrained_1_0_0_RC2
      • BioSimSpace.Parameters.openff_unconstrained_1_0_1
      • BioSimSpace.Parameters.openff_unconstrained_1_1_0
      • BioSimSpace.Parameters.openff_unconstrained_1_1_1
      • BioSimSpace.Parameters.openff_unconstrained_1_2_0
      • BioSimSpace.Parameters.openff_unconstrained_1_2_1
      • BioSimSpace.Parameters.openff_unconstrained_1_3_0
      • BioSimSpace.Parameters.openff_unconstrained_1_3_1
      • BioSimSpace.Parameters.openff_unconstrained_1_3_1_alpha_1
      • BioSimSpace.Parameters.openff_unconstrained_2_0_0
      • BioSimSpace.Parameters.openff_unconstrained_2_0_0_rc_1
      • BioSimSpace.Parameters.openff_unconstrained_2_0_0_rc_2
      • BioSimSpace.Parameters.openff_unconstrained_2_1_0
      • BioSimSpace.Parameters.openff_unconstrained_2_1_0_rc_1
      • BioSimSpace.Parameters.openff_unconstrained_2_1_1
      • BioSimSpace.Parameters.openff_unconstrained_2_2_0
      • BioSimSpace.Parameters.openff_unconstrained_2_2_0_rc1
      • BioSimSpace.Parameters.openff_unconstrained_2_2_1
      • BioSimSpace.Parameters.openff_unconstrained_2_2_1_rc1
      • BioSimSpace.Parameters.parameterise
      • BioSimSpace.Parameters.formalCharge
    • BioSimSpace.Process
      • BioSimSpace.Process.engines
      • BioSimSpace.Process.createProcess
      • BioSimSpace.Process.Amber
      • BioSimSpace.Process.Gromacs
      • BioSimSpace.Process.Namd
      • BioSimSpace.Process.OpenMM
      • BioSimSpace.Process.Plumed
      • BioSimSpace.Process.Somd
      • BioSimSpace.Process.ProcessRunner
    • BioSimSpace.Protocol
      • BioSimSpace.Protocol.protocols
      • BioSimSpace.Protocol.createProtocol
      • BioSimSpace.Protocol.Minimisation
      • BioSimSpace.Protocol.Equilibration
      • BioSimSpace.Protocol.Production
      • BioSimSpace.Protocol.FreeEnergyMinimisation
      • BioSimSpace.Protocol.FreeEnergyEquilibration
      • BioSimSpace.Protocol.FreeEnergyProduction
      • BioSimSpace.Protocol.FreeEnergy
      • BioSimSpace.Protocol.Metadynamics
      • BioSimSpace.Protocol.Steering
      • BioSimSpace.Protocol.Custom
      • BioSimSpace.Protocol.ATMMinimisation
      • BioSimSpace.Protocol.ATMEquilibration
      • BioSimSpace.Protocol.ATMAnnealing
      • BioSimSpace.Protocol.ATMProduction
    • BioSimSpace.Sandpit
    • BioSimSpace.Solvent
      • BioSimSpace.Solvent.solvate
      • BioSimSpace.Solvent.spc
      • BioSimSpace.Solvent.spce
      • BioSimSpace.Solvent.tip3p
      • BioSimSpace.Solvent.tip4p
      • BioSimSpace.Solvent.tip5p
      • BioSimSpace.Solvent.waterModels
    • BioSimSpace.Stream
      • BioSimSpace.Stream.save
      • BioSimSpace.Stream.load
    • BioSimSpace.Trajectory
      • BioSimSpace.Trajectory.Trajectory
    • BioSimSpace.Types
      • BioSimSpace.Types.Angle
      • BioSimSpace.Types.Area
      • BioSimSpace.Types.Charge
      • BioSimSpace.Types.Coordinate
      • BioSimSpace.Types.Energy
      • BioSimSpace.Types.Length
      • BioSimSpace.Types.Pressure
      • BioSimSpace.Types.Temperature
      • BioSimSpace.Types.Time
      • BioSimSpace.Types.Vector
      • BioSimSpace.Types.Volume
    • BioSimSpace.Units
      • BioSimSpace.Units.Length.meter
      • BioSimSpace.Units.Length.angstrom
      • BioSimSpace.Units.Length.nanometer
      • BioSimSpace.Units.Length.picometer
      • BioSimSpace.Units.Area.meter2
      • BioSimSpace.Units.Area.angstrom2
      • BioSimSpace.Units.Area.nanometer2
      • BioSimSpace.Units.Area.picometer2
      • BioSimSpace.Units.Angle.radian
      • BioSimSpace.Units.Angle.degree
      • BioSimSpace.Units.Volume.meter3
      • BioSimSpace.Units.Volume.angstrom3
      • BioSimSpace.Units.Volume.nanometer3
      • BioSimSpace.Units.Volume.picometer3
      • BioSimSpace.Units.Charge.electron_charge
      • BioSimSpace.Units.Charge.coulomb
      • BioSimSpace.Units.Energy.kcal_per_mol
      • BioSimSpace.Units.Energy.kj_per_mol
      • BioSimSpace.Units.Energy.kt
      • BioSimSpace.Units.Pressure.atm
      • BioSimSpace.Units.Pressure.bar
      • BioSimSpace.Units.Temperature.kelvin
      • BioSimSpace.Units.Temperature.celsius
      • BioSimSpace.Units.Temperature.fahrenheit
      • BioSimSpace.Units.Time.day
      • BioSimSpace.Units.Time.hour
      • BioSimSpace.Units.Time.minute
      • BioSimSpace.Units.Time.second
      • BioSimSpace.Units.Time.millisecond
      • BioSimSpace.Units.Time.nanosecond
      • BioSimSpace.Units.Time.picosecond
      • BioSimSpace.Units.Time.femtosecond
    • BioSimSpace._Config
      • BioSimSpace._Config.Amber
      • BioSimSpace._Config.Gromacs
      • BioSimSpace._Config.Somd
    • BioSimSpace._Exceptions
      • BioSimSpace._Exceptions.AlignmentError
      • BioSimSpace._Exceptions.AnalysisError
      • BioSimSpace._Exceptions.ConversionError
      • BioSimSpace._Exceptions.IncompatibleError
      • BioSimSpace._Exceptions.MissingSoftwareError
      • BioSimSpace._Exceptions.ParameterisationError
      • BioSimSpace._Exceptions.StreamError
      • BioSimSpace._Exceptions.ThirdPartyError
    • BioSimSpace._SireWrappers
      • BioSimSpace._SireWrappers.Atom
      • BioSimSpace._SireWrappers.Bond
      • BioSimSpace._SireWrappers.Molecule
      • BioSimSpace._SireWrappers.Molecules
      • BioSimSpace._SireWrappers.Residue
      • BioSimSpace._SireWrappers.System
      • BioSimSpace._SireWrappers.SearchResult
    • BioSimSpace._Utils
      • BioSimSpace._Utils.WorkDir
      • BioSimSpace._Utils.cd
      • BioSimSpace._Utils.command_split
      • BioSimSpace._Utils._module_stub
      • BioSimSpace._Utils._try_import
      • BioSimSpace._Utils._have_imported
      • BioSimSpace._Utils._assert_imported
  • How to ask for help
  • Contributing
    • Developer’s guide
    • Coding Style
    • Development process
    • Creating releases
    • Roadmap
  • Contributors
  • Code of Conduct
  • Changelog
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Detailed Guides¶

Here are some detailed guides that (we hope) will make it easier to use and understand various parts of BioSimSpace.

  • Nodes
    • Writing nodes
    • Running nodes
    • Common Workflow Language
    • Forwards compatibility
    • Examples
  • Protocols
    • Customising protocols
    • Writing protocols
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Last updated on Oct 24, 2024