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Installation
HTMD
Moleculekit
ACEMD
PlayMolecule
More
JobQueues
Help
Internal Docs
Twitter
GitHub
LinkedIn
Youtube
Medium
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.versionwarnings module
HTMD
htmd.projections package
htmd.project...
htmd.projections.metricshell module
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