Skip to main content
Ctrl+K
Logo image

Site Navigation

  • Installation
  • HTMD
  • Moleculekit
  • ACEMD
  • PlayMolecule
  • PlayMolecule-API
  • JobQueues
  • Help
  • Internal Docs
  • Acellera

Site Navigation

  • Installation
  • HTMD
  • Moleculekit
  • ACEMD
  • PlayMolecule
  • PlayMolecule-API
  • JobQueues
  • Help
  • Internal Docs
  • Acellera

Section Navigation

  • Installation
  • Tutorials
    • Introduction to HTMD
      • Python primer
      • Getting started with HTMD
      • HTMD Molecules
      • Visualization in HTMD
    • Building with HTMD
      • Protein preparation
      • Advanced building
      • System building protein-ligand
      • System building protein in Membrane
    • Simulations in HTMD
      • Molecular Dynamics in HTMD
      • Wrapping Simulations
      • Adaptive Sampling Explained
      • Adaptive Sampling Tutorial
      • Adaptive Bandit Tutorial
    • Analysis in HTMD
      • Getting Started with Projections
      • Ligand binding analysis
      • Protein folding analysis
      • CXCL12 conformational analysis
    • Advanced uses
      • System building Protein-Protein
      • Using docking to initialize positions
      • Equilibration protocol for the mu opioid GPCR
    • Tools
      • Maximal Substructural Alignment
      • Sequence Based Alignment
      • FFEvaluate
      • Membrane Builder
    • Changelog
  • Documentation
    • Molecule
    • Building
      • System preparation
      • Solvating
      • CHARMM builder
      • AMBER builder
    • MD Simulations
      • MD Engines
        • htmd.mdengine.acemd package
      • Queues
        • jobqueues.celeryfiles package
        • jobqueues.celeryqueue module
        • jobqueues.config module
        • jobqueues.home module
        • jobqueues.localqueue module
        • jobqueues.lsfqueue module
        • jobqueues.pbsqueue module
        • jobqueues.playqueue module
        • jobqueues.sgequeue module
        • jobqueues.simqueue module
        • jobqueues.slurmqueue module
        • jobqueues.util module
      • Adaptive sampling
        • Adaptive sampling
      • State-of-the-art protocols for molecular simulations
        • htmd.protocols.equilibration_v3 module
        • htmd.protocols.production_v6 module
    • Simulation List
    • Projections
      • MetricData - Storage for projected data
      • Metric - Helper class for combining Metrics for projection
      • MetricCoordinate - coordinates of an atom selection
      • MetricDistance - (Self-)distance-based metrics between atoms selections
      • MetricDihedral - Dihedral-based metrics
      • MetricRmsd - RMSD-based metric
      • MetricShell - occupancy of an atom selection (e.g. water) around another selection
      • MetricSecondaryStructure - secondary structure-based metric
      • MetricPlumed2 - access all Plumed2 metrics (CVs)
      • MetricSasa - Solvent accessible surface area
      • MetricTMscore - TMscore-based metric
      • MetricFluctuation - RMSF-based metric
    • Dimensionality Reduction
      • TICA - Time independent component analysis
      • KMeansTri - kmeans triangle inequality
      • GWPCA Principal Component Analysis
    • Clustering
      • KCenters clustering method
      • RegCluster regular sized clustering
    • Markov state models
    • Kinetics
  • API
    • htmd.adaptive package
      • htmd.adaptive.adaptive module
      • htmd.adaptive.adaptivebandit module
      • htmd.adaptive.adaptivegoal module
      • htmd.adaptive.adaptivegoaleg module
      • htmd.adaptive.adaptiverun module
      • htmd.adaptive.util module
    • htmd.builder package
      • htmd.builder.amber module
      • htmd.builder.builder module
      • htmd.builder.charmm module
      • htmd.builder.ionize module
      • htmd.builder.loopmodeler module
      • htmd.builder.noncanonical module
      • htmd.builder.solvate module
    • htmd.clustering package
      • htmd.clustering.kcenters module
      • htmd.clustering.regular module
    • htmd.mdengine package
      • htmd.mdengine.acemd package
        • htmd.mdengine.acemd.acemd module
    • htmd.membranebuilder package
      • htmd.membranebuilder.build_membrane module
      • htmd.membranebuilder.globalminimization module
      • htmd.membranebuilder.ljfluid module
      • htmd.membranebuilder.pdbreporter module
      • htmd.membranebuilder.ringpenetration module
      • htmd.membranebuilder.simulate_openmm module
    • htmd.molecule package
      • htmd.molecule.molecule module
      • htmd.molecule.util module
    • htmd.projections package
      • htmd.projections.gwpca module
      • htmd.projections.kmeanstri module
      • htmd.projections.metric module
      • htmd.projections.metriccoordinate module
      • htmd.projections.metricdihedral module
      • htmd.projections.metricdistance module
      • htmd.projections.metricfluctuation module
      • htmd.projections.metricplumed2 module
      • htmd.projections.metricrmsd module
      • htmd.projections.metricsasa module
      • htmd.projections.metricsecondarystructure module
      • htmd.projections.metricshell module
      • htmd.projections.metricsphericalcoordinate module
      • htmd.projections.metrictmscore module
      • htmd.projections.tica module
    • htmd.protocols package
      • htmd.protocols.equilibration_v3 module
      • htmd.protocols.production_v6 module
    • htmd.queues package
      • htmd.queues.localqueue module
      • htmd.queues.lsfqueue module
      • htmd.queues.pbsqueue module
      • htmd.queues.playqueue module
      • htmd.queues.simqueue module
      • htmd.queues.slurmqueue module
    • htmd.config module
    • htmd.decorators module
    • htmd.dock module
    • htmd.home module
    • htmd.kinetics module
    • htmd.latest module
    • htmd.license module
    • htmd.metricdata module
    • htmd.metricdatagenerator module
    • htmd.model module
    • htmd.mutualinformation module
    • htmd.parallelprogress module
    • htmd.pathplanning module
    • htmd.session module
    • htmd.simlist module
    • htmd.ui module
    • htmd.units module
    • htmd.util module
    • htmd.version module
    • htmd.versionwarnings module
  • HTMD
  • htmd package
  • htmd.molecule package

htmd.molecule package#

Submodules#

  • htmd.molecule.molecule module
  • htmd.molecule.util module

Module contents#

previous

htmd.membranebuilder.simulate_openmm module

next

htmd.molecule.molecule module
On this page
  • Submodules
  • Module contents

© Copyright Acellera 2023.