PLUMED-TUTORIALS

maze Tutorial

A PLUMED tutorial to run ligand unbinding trajectories with maze. The original work, which explains the background of maze simulations, is published in [1]. Implementation details are summarized in [2].

This tutoral uses a recent implementation of maze which differs from the original one.

The new version is accessible here and will be merged into PLUMED soon. For information on how to compile it, see here. The maze module must be enabled during compilation.

This tutorial covers the following:

Background

A brief introduction to the background behind the use of maze.

L99A T4 Lysozyme-Benzene

A case study for this tutorial is a small protein that binds benzene.

Input files preparation

Input setup for maze.

Results

Presentation of results obtained with maze.

[1] J. Rydzewski, and O. Valsson, Finding Multiple Reaction Pathways of Ligand Unbinding J. Chem. Phys. 150, 221101 (2019) doi:10.1063/1.5108638.

[2] J. Rydzewski, maze: Heterogeneous Ligand Unbinding along Transient Protein Tunnels Comp. Phys. Commun. 247, 106865 (2020) doi:10.1016/j.cpc.2019.106865.

flowchart
  A[PLUMED syntax] -.-> B[Background];
  B --> C[System]
  C --> D[Input files]
  D --> E[Results]
  
  click A "../../../21/001/data/NAVIGATION.html" "This lesson teaches the basic features of the PLUMED input syntax."
  click B "background.html" "Background and introduction to maze."
  click C "system.html" "System: L99A T4 Lysozyme-Benzene."
  click D "input.html" "Input files preparation."
  click E "results.html" "Results."

Click here to open manual pages for actions discussed in this tutorial.