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acelleralive
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Contents
HTMD
Installation
User Guide
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
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
HTMD 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
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
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
ACEMD3
Capabilities
Not available capabilities
Performance
Speed benchmarks
Release notes
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
Migrating from the old
ACEMD
Reference
Command line arguments
Input file options
Force field
Iteractions
Restraints
Initial state
Minimization
Integrator
Thermostat
Barostat
Output
Licence
Support
ACEMD (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
Version:
latest
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htmd.projections.metrictmscore module
htmd.projections.metrictmscore module
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