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Contents
HTMD
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
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
1.12.0 (stable) - 2018/03/22
1.10.0 (stable) - 2017/10/25
1.8.0 (stable) - 2017/07/17
1.6.0 (stable) - 2017/03/01
Documentation
Molecule
Building
Solvating
Protein preparation
CHARMM builder
AMBER builder
MD Simulations
Applications
Adaptive sampling
State-of-the-art protocols for molecular simulations
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
Subpackages
htmd.adaptive package
htmd.apps package
htmd.builder package
htmd.clustering package
htmd.membranebuilder package
htmd.molecule package
htmd.projections package
htmd.protocols package
htmd.queues package
Submodules
htmd.config module
htmd.decorators module
htmd.dock module
htmd.home module
htmd.kinetics module
htmd.kineticshmm module
htmd.latest module
htmd.metricdata module
htmd.model module
htmd.modelhmm module
htmd.mutualinformation module
htmd.numbautil 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
Module contents
Developer’s Guide
How to contribute
Introduction
How to Contribute Fixes
How to Contribute New Features
Contributor Agreement
List of Features Interesting for HTMD
Guidelines for developers
Coding Style Tips
Using modules inside HTMD
Using Docstrings and Doctests
Versioning
HTMD Versions Explained
How to release a new HTMD version?
Moleculekit
Installation
Downloading miniconda
Create a conda environment
Install with pip
Install with conda
The Molecule class
The SmallMol class
Molecule tools
Contents
Protein segmentation: Automatically detects and assigns segments in proteins
Protein preparation: Protonates proteins and optimizes hbond networks
Sequence-based structure alignment: Aligns two protein structures by their sequence alignment
Voxel Descriptors: Calculates 3D voxels channels containing features of a Molecule or SmallMol
Maximal substructure alignment: Aligns two small molecules by their maximal substructure
Projections
Contents
MetricCoordinate: xyz coordinate projection
MetricDihedral: dihedral angles projection
MetricDistance: atom distances/contacts projection
MetricFluctuation: atom position fluctuations
MetricPlumed2: support for Plumed2 projections
MetricRmsd: root mean square deviation of structures to a reference
MetricSasa: solvent accessible surface area projection
MetricSecondaryStructure: protein secondary structure projection
MetricShell: density of atoms in shells around other atoms
MetricSphericalCoordinate: spherical coordinates of two COMs
MetricTMscore: TMscore projection
Tutorials
Contents
Voxelization
ACEMD v3
Capabilities
Not available capabilities
Performance
Speed benchmarks
Release notes
3.3.0 (2020-06-23)
3.2.4 (2020-04-23)
3.2.3 (2019-11-12)
3.2.2 (2019-10-08)
3.2.1 (2019-09-20)
3.2.0 (2019-08-27)
3.1.2 (2019-06-04)
3.1.1 (2019-05-08)
3.1.0 (2019-04-18)
3.0.4 (2019-02-27)
3.0.3 (2019-02-25)
3.0.2 (2018-03-28)
3.0.1 (2017-12-18)
3.0.0 (2017-12-12)
Installation
Dependencies
Tutorial
Molecular dynamics simulation of DHFR
Metadynamics simulation of alaninde dipeptide
Migrating from the old
ACEMD
Manual
Command line arguments
Input file options
Force field
Iteractions
Restraints
Metadynamics
Initial state
Minimization
Integrator
Thermostat
Barostat
Output
Licence
Support
ACEMD v2 (deprecated)
ACEMD Manual
Introduction
Fundamental units
Force field parameters
Running ACEMD
Specifying an Input File
Command Help
Selecting a GPU
Running parallel ensembles
Simulation Configuration
Quick Configurations
NVT vs NPT ensemble
Input Files
Output Files
Standard output
Restarting
Advanced material
Tcl Scripting
Debug TCL scripts
PLUMED library
Plugin interface
Getting support
Citations
ACEMD Command Reference
Configuration
Input
Output
Forcefield
Charmm
Amber
Martini
Electrostatics
Barostat
Thermostat
Constraints
External Forces
Minimisation
Interactive
Extensions
TCL Extension
Analysis
Parameterize
Method
Tutorial
Prepare molecule
Get command-line options
Positional Arguments
Named Arguments
Set total charge
Choose force field
Atomic charges
List parameterizable dihedral angles
Choose QM code
Choose QM level
Control the execution of QM calculations
Reuse QM and re-parametrize
Find and validate parameters
Usage
Positional Arguments
Named Arguments
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