Welcome to AdaptivePELE’s documentation!

AdaptivePELE is a Python module to perform enhancing sampling of molecular simulation built around the Protein Energy Landscape Exploration method (PELE) developed in the Electronic and Atomic Protein Modelling grop (EAPM) at the Barcelona Supercomputing Center (BSC). AdaptivePELE’s code is publicly available in GitHub under the MIT license.

Contributors

Daniel Lecina, Joan Francesc Gilabert, Oriol Gracia, Daniel Soler

Mantainer

Joan Francesc Gilabert (cescgina@gmail.com)

Contents

• User Manual
  • Installation
  • Overview
  • Control file outline
  • GeneralParams block
  • Simulation block
  • Clustering block
  • Spawning block
  • Control File Examples
  • Output
  • Analysis
  • Dynamical hooks
  • Non-PDB trajectories
  • Input preparation for MD
  • Equilibration procedure in MD
  • Running AdaptivePELE with GPUs
• Frequently Asked Questions
• AdaptivePELE – Package Description
  • adaptiveSampling Module
  • automateRoundsAdaptive Module
  • Subpackages
• Changelog
  • 1.7.2 - Unreleased
  • 1.7.1 - 2021-05-14
  • 1.7 - 2021-02-11
  • 1.6.3 - 2020-09-28
  • 1.6.2 - 2019-07-24
  • 1.6.1 - 2019-04-26
  • 1.6 - 2019-02-19
  • 1.5.2 - 2018-08-13
  • 1.5.1 - 2018-06-07
  • 1.5 - 2018-05-11
  • 1.4.2 - 2018-03-02
  • 1.4 - 2018-01-30
  • 1.3 - 2017-06-01
  • 1.2 - 2017-05-09
  • 1.1 - 2017-02-17
  • 1.0 - 2017-01-19

Indices and tables

• Index

• Module Index

• Search Page