HTMD

What is it?

HTMD is a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyze molecular systems. HTMD is based on Python, so scientists can easily extend it to their needs. With HTMD is possible to do very complex protocols in just few lines.

In a single script, it is possible to plan an entire computational experiment, from manipulating PDBs, building, executing and analyzing simulations, computing Markov state models, kinetic rates, affinities and pathways.

Citing HTMD:

If you are using HTMD in your publications please cite following papers:

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

S. Doerr, M. J. Harvey, Frank Noé, and G. De Fabritiis

Journal of Chemical Theory and Computation 2016 12 (4), 1845-1852

DOI: 10.1021/acs.jctc.6b00049.

Where to start

The user guide is a good place to start playing around.

• Installation
  • Installing HTMD
• Tutorials
  • Introduction to HTMD
    • Python primer
      • Why Python?
      • HTMD relation to Python and Miniconda
      • Programming basics with Python
      • Python Interpreters and writing Python code
      • Jupyter Notebooks
        • Extra: IPython built-in magic commands
      • Python modules usage
      • os module and glob function: interacting with the filesystem
      • General Programming Overview
        • Strings
        • Relational operators
        • Lists of objects (integers, strings…)
        • Conditionals (if-clause)
        • Loops (for-loop)
      • Numpy: the best way to handle arrays
        • Array multiplication
        • Sequences
        • Slicing
        • More matrix operations
        • Other numpy operations
      • Functions
      • Variables and Objects
      • Identity of an object
      • Argument passing
      • Plots using matplotlib module
      • Getting Help
      • Debugging code in notebooks
      • Python Exercises
    • Getting started with HTMD
      • Reading files
      • Writing files
      • Looking inside a Molecule
      • Properties and methods of Molecule objects
    • HTMD Molecules
      • Molecule getters and setters
      • Check the residue IDs of Cysteines in the Molecule
      • Retrieve the coordinates of atoms
      • Know the chains or segments present in the Molecule
      • Set properties of the Molecule
      • Count the number of waters in the Molecule
      • Duplicate, modify and write Molecule objects
      • Joining molecules/segments
      • Playing with coordinates
      • Rotations
      • Working with MD trajectories
      • Biochemistry of HTMD Molecules
      • Exercise 1: find residues in contact with a ligand
      • Exercise 2: find duplicate residues
        • Solution 1.
        • Solution 2.
      • Exercise 3: find gaps in the sequence of residue numbers
    • Visualization in HTMD
      • On-the-fly molecule visualization and interaction
      • The “quick” or “transient” view
      • The “explicit” way: using Molecule.reps
      • Atom selection expressions work as in VMD
      • Visualizing a trajectory
  • Building with HTMD
    • Protein preparation
      • What is system preparation?
      • Let’s start
      • System Preparation in HTMD
        • Protein residue pKas in water
        • Modified residue names
        • Limitations
      • systemPrepare function
        • Parameters
        • Example
        • Visualize protonation of residue 40
      • Preparation report
      • Special case: Membrane proteins
      • Case 2. Building with a ligand
      • Case 3. Membrane proteins
      • Citations
    • System building protein-ligand
      • Load the protein-ligand complex
      • Clean the structures
      • Preparing the protein
      • Define segments
      • Let’s work on the ligand!
      • Let’s randomize the ligand position
        • Mix it all together
      • Solvate
      • Build the System with a specific forcefield
        • CHARMM forcefield
        • Build and ionize using CHARMM
        • AMBER forcefield
        • Build and ionize using Amber
      • Visualize
    • System building protein in Membrane
      • Prepare the protein
      • Add a sodium atom in the receptor
      • Embed the protein into a membrane
      • Visualize the embedded system
      • Add a ligand
      • Put it in a water box
      • Visualize
      • Build with AMBER
      • Visualize built system
    • System building for protein-protein interaction
      • Download the two proteins and view them
      • Filter the structures to keep only one chain of each
      • Visualize the filtered structures
      • Mutate modified residues
      • Assignments and renaming
      • Combine the proteins and center them
      • Solvate the combined system
      • Build the solvated system in AMBER
      • Visualize the built system
  • Simulations in HTMD
    • Molecular Dynamics in HTMD
      • Build a sample system
      • Equilibration protocol
      • Run the equilibration
      • Production protocol
      • Run the production
      • Quickly visualize the trajectory
    • Wrapping Simulations
      • Periodic boundary conditions (PBC)
        • What does this mean?
        • Example
      • Storing of coordinates during a simulation
        • Example
      • Wrapping
        • How does wrapping work?
        • How to select the ideal wrapping center?
      • How do I wrap?
    • Adaptive Sampling Explained
      • Concept
      • Unit of execution
      • How to start
      • Simulation length
      • Simulation details
      • Adaptive script example
      • Execution in a notebook
      • Setting a simple cron job
      • Visualizing the starting conformations
    • Adaptive Sampling Tutorial
      • Get the generators folder structure
      • Adaptive classes
      • AdaptiveMD
      • AdaptiveGoal
      • The goal function
        • RMSD goal function
        • Functions with multiple arguments
        • Other goal function examples
    • Adaptive Bandit Tutorial
      • Concept
      • Getting started
      • AdaptiveBandit
    • Equilibration protocol for the mu opioid GPCR
      • Build
      • Equilibrate
      • Production
  • Analysis in HTMD
    • Getting Started with Projections
      • Projecting simulations
      • Projecting single Molecule objects
        • Getting the RMSD along time
        • Plot the RMSD along time
      • Projecting a list of MD simulations
        • Use Metric class to project a list of simulations
      • Working with MetricData objects
        • Operations and calculations
        • Playing with the projection mapping
    • Ligand binding analysis
      • Getting started
      • Creating a simulation list
      • Filtering trajectories
      • Calculating metrics
      • Removing trajectories
      • TICA
      • Bootstrapping
      • Clustering conformations
      • Building the Markov model
      • Visualizing the states
      • Calculating the kinetics
    • Protein folding analysis
      • Getting started
      • Creating a simulation list
      • Filtering trajectories
      • Calculating metrics
      • Removing trajectories
      • TICA
      • Bootstrapping
      • Clustering conformations
      • Building the Markov model
      • Visualizing the states
      • Calculating the kinetics
    • CXCL12 conformational analysis
      • Getting started
      • Introduction to CXCL12
      • Sampling major conformational states
      • Load the trajectories into a simlist
      • Calculate metrics: protein backbone dihedrals
      • Dimensionality reduction
      • Clustering
      • MSM analysis and visualization
      • Build Markov Model
      • Statistics: What are the major differences between the states X and Y?
      • Mapping back: Which trajectory originated the state X?
      • Studying a defined reaction coordinate
      • tICA projection
      • Clustering
      • Plot timescales
      • Build a Markov Model
      • Visualize states
      • Analyse Open Conformation
      • Calculate RMSD of the site of interest for a selected trajectory
      • Do you see the pocket opening at 50ns?
      • Visualize the trajectory from your browser
  • Tools
    • Maximal Substructural Alignment
      • Quick Example
      • Detailed explanation
    • Sequence Based Alignment
      • Quick Example
      • Detailed Explanation
    • FFEvaluate
      • Quick example
      • Detailed explanation
      • Disclaimers
    • Membrane Builder
      • Quick example
      • Detailed explanation
      • Adding new lipids
    • Using docking to initialize positions
      • Dock the protein with the ligand
        • Visualize the docked poses
      • Build systems from docked poses
      • Equilibrate the build systems
      • Create the production folder
• Documentation
  • Molecule
    • Molecule
      • Molecule.numAtoms
      • Molecule.numFrames
      • Molecule.numResidues
      • Molecule.record
      • Molecule.serial
      • Molecule.name
      • Molecule.altloc
      • Molecule.resname
      • Molecule.chain
      • Molecule.resid
      • Molecule.insertion
      • Molecule.occupancy
      • Molecule.beta
      • Molecule.segid
      • Molecule.element
      • Molecule.charge
      • Molecule.masses
      • Molecule.atomtype
      • Molecule.formalcharge
      • Molecule.coords
      • Molecule.box
      • Molecule.boxangles
      • Molecule.bonds
      • Molecule.bondtype
      • Molecule.angles
      • Molecule.dihedrals
      • Molecule.impropers
      • Molecule.crystalinfo
      • Molecule.frame
      • Molecule.fileloc
      • Molecule.time
      • Molecule.fstep
      • Molecule.reps
      • Molecule.viewname
      • Molecule.addBond()
      • Molecule.align()
      • Molecule.alignBySequence()
      • Molecule.append()
      • Molecule.appendFrames()
      • Molecule.atomselect()
      • Molecule.center()
      • Molecule.copy()
      • Molecule.deleteBonds()
      • Molecule.dropFrames()
      • Molecule.empty()
      • Molecule.filter()
      • Molecule.frame
      • Molecule.fromDict()
      • Molecule.fstep
      • Molecule.get()
      • Molecule.getCenter()
      • Molecule.getDihedral()
      • Molecule.getNeighbors()
      • Molecule.guessBonds()
      • Molecule.hasBond()
      • Molecule.insert()
      • Molecule.moveBy()
      • Molecule.mutateResidue()
      • Molecule.numAtoms
      • Molecule.numBonds
      • Molecule.numFrames
      • Molecule.numResidues
      • Molecule.read()
      • Molecule.remove()
      • Molecule.removeBond()
      • Molecule.renumberResidues()
      • Molecule.reorderAtoms()
      • Molecule.rotateBy()
      • Molecule.sequence()
      • Molecule.set()
      • Molecule.setDihedral()
      • Molecule.toDict()
      • Molecule.toGraph()
      • Molecule.toOpenFFMolecule()
      • Molecule.translateBy()
      • Molecule.view()
      • Molecule.wrap()
      • Molecule.write()
      • Molecule.x
      • Molecule.y
      • Molecule.z
    • Representations
      • Representations.add()
      • Representations.append()
      • Representations.list()
      • Representations.remove()
    • TopologyInconsistencyError
    • UniqueAtomID
      • UniqueAtomID.fromMolecule()
      • UniqueAtomID.selectAtom()
    • UniqueResidueID
      • UniqueResidueID.fromMolecule()
      • UniqueResidueID.selectAtoms()
    • calculateUniqueBonds()
    • getBondedGroups()
    • mol_equal()
  • Building
    • System preparation
      • proteinPrepare()
      • systemPrepare()
    • Solvating
      • solvate()
    • CHARMM builder
      • build()
      • cleanup_charmm_prm()
      • combine()
      • defaultParam()
      • defaultStream()
      • defaultTopo()
      • htmdCharmmHome()
      • listFiles()
      • search()
      • split()
    • AMBER builder
      • build()
      • defaultAmberHome()
      • defaultFf()
      • defaultParam()
      • defaultTopo()
      • htmdAmberHome()
      • listFiles()
  • MD Simulations
    • Queues
      • Subpackages
        • jobqueues.celeryfiles package
      • Submodules
        • 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
      • Module contents
    • Adaptive sampling
      • Adaptive sampling
        • AdaptiveMD
  • Simulation List
    • Frame
      • Frame.frame
      • Frame.piece
      • Frame.sim
    • Sim
      • Sim.simid
      • Sim.parent
      • Sim.input
      • Sim.trajectory
      • Sim.molfile
      • Sim.numframes
      • Sim.copy()
      • Sim.fromHDF5()
      • Sim.toHDF5()
    • simfilter()
    • simlist()
    • simmerge()
  • Projections
    • MetricData - Storage for projected data
      • MetricData
        • MetricData.trajectories
        • MetricData.fstep
        • MetricData.description
        • MetricData.K
        • MetricData.N
        • MetricData.Centers
        • MetricData.St
        • MetricData.abs2rel()
        • MetricData.abs2sim()
        • MetricData.aggregateTime
        • MetricData.append()
        • MetricData.bootstrap()
        • MetricData.cluster()
        • MetricData.combine()
        • MetricData.copy()
        • MetricData.dat
        • MetricData.deconcatenate()
        • MetricData.dropDimensions()
        • MetricData.dropFrames()
        • MetricData.dropTraj()
        • MetricData.fromHDF5()
        • MetricData.load()
        • MetricData.map
        • MetricData.numDimensions
        • MetricData.numFrames
        • MetricData.numTrajectories
        • MetricData.plotClusters()
        • MetricData.plotCounts()
        • MetricData.plotTrajSizes()
        • MetricData.ref
        • MetricData.rel2sim()
        • MetricData.sampleClusters()
        • MetricData.sampleRegion()
        • MetricData.save()
        • MetricData.simlist
        • MetricData.splitCols()
        • MetricData.toHDF5()
        • MetricData.trajLengths
      • Trajectory
        • Trajectory.cluster
        • Trajectory.copy()
        • Trajectory.dropFrames()
        • Trajectory.fromHDF5()
        • Trajectory.numDimensions
        • Trajectory.numFrames
        • Trajectory.projection
        • Trajectory.reference
        • Trajectory.toHDF5()
    • Metric - Helper class for combining Metrics for projection
      • Metric
        • Metric.getMapping()
        • Metric.project()
        • Metric.set()
    • MetricCoordinate - coordinates of an atom selection
      • MetricCoordinate
        • MetricCoordinate.getMapping()
        • MetricCoordinate.project()
    • MetricDistance - (Self-)distance-based metrics between atoms selections
      • MetricDistance
        • MetricDistance.getMapping()
        • MetricDistance.project()
      • MetricSelfDistance
      • contactVecToMatrix()
      • reconstructContactMap()
    • MetricDihedral - Dihedral-based metrics
      • AtomNotFoundException
      • Dihedral
        • Dihedral.chi1()
        • Dihedral.chi2()
        • Dihedral.chi3()
        • Dihedral.chi4()
        • Dihedral.chi5()
        • Dihedral.dihedralsToIndexes()
        • Dihedral.omega()
        • Dihedral.phi()
        • Dihedral.proteinDihedrals()
        • Dihedral.psi()
      • MetricDihedral
        • MetricDihedral.getMapping()
        • MetricDihedral.project()
    • MetricRmsd - RMSD-based metric
      • MetricRmsd
        • MetricRmsd.getMapping()
        • MetricRmsd.project()
    • MetricShell - occupancy of an atom selection (e.g. water) around another selection
      • MetricShell
        • MetricShell.getMapping()
        • MetricShell.project()
    • MetricSecondaryStructure - secondary structure-based metric
      • MetricSecondaryStructure
        • MetricSecondaryStructure.getMapping()
        • MetricSecondaryStructure.project()
    • MetricPlumed2 - access all Plumed2 metrics (CVs)
      • MetricPlumed2
        • MetricPlumed2.getMapping()
        • MetricPlumed2.project()
      • PlumedCOM
      • PlumedCV
        • PlumedCV.genTemplate()
      • PlumedGenericGroup
      • PlumedGroup
      • PlumedMolinfo
      • PlumedStatement
      • PlumedVerbatim
      • genTemplate()
      • manual()
    • MetricSasa - Solvent accessible surface area
      • MetricSasa
        • MetricSasa.getMapping()
        • MetricSasa.project()
    • MetricTMscore - TMscore-based metric
      • MetricTMscore
        • MetricTMscore.getMapping()
        • MetricTMscore.project()
    • MetricFluctuation - RMSF-based metric
      • MetricFluctuation
        • MetricFluctuation.getMapping()
        • MetricFluctuation.project()
  • Dimensionality Reduction
    • TICA - Time independent component analysis
      • TICA
        • TICA.project()
    • KMeansTri - kmeans triangle inequality
      • KMeansTri
        • KMeansTri.project()
    • GWPCA Principal Component Analysis
      • GWPCA
        • GWPCA.project()
  • Clustering
    • KCenters clustering method
      • KCenter
        • KCenter.cluster_centers
        • KCenter.centerFrames
        • KCenter.labels_
        • KCenter.clusterSize_
        • KCenter.distance
        • KCenter.fit()
        • KCenter.set_fit_request()
    • RegCluster regular sized clustering
      • RegCluster
        • RegCluster.cluster_centers
        • RegCluster.centerFrames
        • RegCluster.labels_
        • RegCluster.clusterSize_
        • RegCluster.clusterSize
        • RegCluster.cluster_centers_
        • RegCluster.fit()
        • RegCluster.set_fit_request()
  • Markov state models
    • Model
      • Model.P
      • Model.cktest()
      • Model.cluster_ofmicro
      • Model.copy()
      • Model.createCoreSetModel()
      • Model.createState()
      • Model.eqDistribution()
      • Model.getStates()
      • Model.load()
      • Model.macro_ofcluster
      • Model.macro_ofmicro
      • Model.macronum
      • Model.markovModel()
      • Model.maxConnectedLag()
      • Model.micro_ofcluster
      • Model.micronum
      • Model.plotFES()
      • Model.plotTimescales()
      • Model.sampleStates()
      • Model.save()
      • Model.viewStates()
    • getStateStatistic()
    • macroAccumulate()
  • Kinetics
    • Kinetics
      • Kinetics.getRates()
      • Kinetics.plotFluxPathways()
      • Kinetics.plotMarkovModel()
      • Kinetics.plotRates()
    • Rates
      • Rates.mfpton
      • Rates.mfptoff
      • Rates.kon
      • Rates.koff
      • Rates.kdeq
      • Rates.g0eq
• API
  • Subpackages
    • htmd.adaptive package
      • Submodules
        • htmd.adaptive.adaptive module
        • htmd.adaptive.adaptivebandit module
        • htmd.adaptive.adaptivegoal module
        • htmd.adaptive.adaptivegoaleg module
        • htmd.adaptive.adaptiverun module
        • htmd.adaptive.util module
      • Module contents
    • htmd.builder package
      • Submodules
        • 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
      • Module contents
    • htmd.clustering package
      • Submodules
        • htmd.clustering.kcenters module
        • htmd.clustering.regular module
      • Module contents
    • htmd.mdengine package
      • Subpackages
        • htmd.mdengine.acemd package
      • Module contents
    • htmd.membranebuilder package
      • Submodules
        • htmd.membranebuilder.build_membrane module
        • htmd.membranebuilder.globalminimization module
        • htmd.membranebuilder.ljfluid module
        • htmd.membranebuilder.ringpenetration module
      • Module contents
    • htmd.projections package
      • Submodules
        • htmd.projections.gwpca module
        • htmd.projections.kmeanstri module
        • htmd.projections.metric module
        • htmd.projections.tica module
      • Module contents
    • htmd.protocols package
      • Submodules
        • htmd.protocols.equilibration_v3 module
        • htmd.protocols.production_v6 module
      • Module contents
  • Submodules
    • htmd.config module
      • config()
    • htmd.decorators module
    • htmd.dock module
      • dock()
    • htmd.home module
      • home()
    • htmd.kinetics module
      • Kinetics
        • Kinetics.getRates()
        • Kinetics.plotFluxPathways()
        • Kinetics.plotMarkovModel()
        • Kinetics.plotRates()
      • Rates
        • Rates.mfpton
        • Rates.mfptoff
        • Rates.kon
        • Rates.koff
        • Rates.kdeq
        • Rates.g0eq
    • htmd.latest module
      • compareVersions()
    • htmd.license module
      • check_for_license()
      • htmd_register()
      • htmd_registration()
      • htmd_show_news()
    • htmd.metricdata module
      • MetricData
        • MetricData.trajectories
        • MetricData.fstep
        • MetricData.description
        • MetricData.K
        • MetricData.N
        • MetricData.Centers
        • MetricData.St
        • MetricData.abs2rel()
        • MetricData.abs2sim()
        • MetricData.aggregateTime
        • MetricData.append()
        • MetricData.bootstrap()
        • MetricData.cluster()
        • MetricData.combine()
        • MetricData.copy()
        • MetricData.dat
        • MetricData.deconcatenate()
        • MetricData.dropDimensions()
        • MetricData.dropFrames()
        • MetricData.dropTraj()
        • MetricData.fromHDF5()
        • MetricData.load()
        • MetricData.map
        • MetricData.numDimensions
        • MetricData.numFrames
        • MetricData.numTrajectories
        • MetricData.plotClusters()
        • MetricData.plotCounts()
        • MetricData.plotTrajSizes()
        • MetricData.ref
        • MetricData.rel2sim()
        • MetricData.sampleClusters()
        • MetricData.sampleRegion()
        • MetricData.save()
        • MetricData.simlist
        • MetricData.splitCols()
        • MetricData.toHDF5()
        • MetricData.trajLengths
      • Trajectory
        • Trajectory.cluster
        • Trajectory.copy()
        • Trajectory.dropFrames()
        • Trajectory.fromHDF5()
        • Trajectory.numDimensions
        • Trajectory.numFrames
        • Trajectory.projection
        • Trajectory.reference
        • Trajectory.toHDF5()
    • htmd.metricdatagenerator module
      • MetricDataGenerator
        • MetricDataGenerator.newMetricData()
        • MetricDataGenerator.newTrajectoriesClusterJumping()
        • MetricDataGenerator.newTrajectoriesFiller()
        • MetricDataGenerator.newTrajectoriesMSM()
        • MetricDataGenerator.newTrajectoriesSimple()
        • MetricDataGenerator.parallelTest()
      • abs2rel()
    • htmd.model module
      • Model
        • Model.P
        • Model.cktest()
        • Model.cluster_ofmicro
        • Model.copy()
        • Model.createCoreSetModel()
        • Model.createState()
        • Model.eqDistribution()
        • Model.getStates()
        • Model.load()
        • Model.macro_ofcluster
        • Model.macro_ofmicro
        • Model.macronum
        • Model.markovModel()
        • Model.maxConnectedLag()
        • Model.micro_ofcluster
        • Model.micronum
        • Model.plotFES()
        • Model.plotTimescales()
        • Model.sampleStates()
        • Model.save()
        • Model.viewStates()
      • getStateStatistic()
      • macroAccumulate()
    • htmd.mutualinformation module
      • MutualInformation
        • MutualInformation.calculate()
        • MutualInformation.loadMI()
        • MutualInformation.saveMI()
        • MutualInformation.save_graphml()
        • MutualInformation.weightGraph()
    • htmd.parallelprogress module
      • ParallelExecutor()
    • htmd.pathplanning module
      • Tree
        • Tree.addPoint()
      • parallelfunc()
      • raytracing()
      • rrt()
      • rrtstarsmart()
    • htmd.session module
      • htmdload()
      • htmdsave()
    • htmd.simlist module
      • Frame
        • Frame.frame
        • Frame.piece
        • Frame.sim
      • Sim
        • Sim.simid
        • Sim.parent
        • Sim.input
        • Sim.trajectory
        • Sim.molfile
        • Sim.numframes
        • Sim.copy()
        • Sim.fromHDF5()
        • Sim.toHDF5()
      • simfilter()
      • simlist()
      • simmerge()
    • htmd.ui module
    • htmd.units module
      • convert()
    • htmd.util module
      • assertSameAsReferenceDir()
      • diffMolecules()
      • ensurelist()
      • getPdbStrings()
      • tempname()
      • testDHFR()
    • htmd.versionwarnings module
  • Module contents

Indices and tables

• Index

• Module Index