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Suite of WESTPA tutorials: Supplementary information

This collection of files is a companion to the Suite of WESTPA tutorials manuscript published in LiveCoMS. Each tutorial directory contains all files necessary for completing that tutorial. Programs such as WESTPA, Amber, Python etc. will need to be installed by the user and are not provided herein. The following is a list of all tutorials with their classification.

Basic tutorial

Please note: in order to successfully complete this tutorial, users will have to create a custom conda environment containing WESTPA, OpenMM and MDTraj. Please see the relevant section on the installation page for how to do this.

  • Na+/Cl- molecular association (OpenMM 7.4, Amber 18 CPU, Amber 18 GPU)

Intermediate tutorial

  • P53 peptide conformational sampling (Amber 18)

Advanced tutorials

  • Chignolin protein folding (Amber 18)

  • WExplore K+ 18-crown-6-ether association (GROMACS 2016.2)

Analysis tutorials

  • Calculating progress coordinates using MDAnalysis/MDTraj

  • The w_ipa suite of analysis tools

  • Dataset visualization and movie-making