MD DaVis

Introduction

MD DaVis is a tool for comparative analysis of molecular dynamics simulations of proteins.

Documentation: https://md-davis.readthedocs.io

Features

1. Free energy landscape
2. Residue properties plot
3. Surface electrostatics
4. Electric field dynamics
5. H-bond/Contact matrix

System Requirements

• A 64-bit operating system
• A Python 3 installation with version ≥ 3.7

Installation

The easiest installation method is with Anaconda or Miniconda. It is highly recommended to install MD DaVis in a virtual environment. The environment.yml is provided to ease the process.

conda env create -f environment.yml -n md_davis_env

This automatically creates a conda environment called md_davis_env with all required dependencies. Activate the environment and install MD DaVis in it using:

conda activate md_davis_env
pip install md-davis

For detailed installation instructions, see: https://md-davis.readthedocs.io/en/latest/install.html

Dependencies

The following dependencies will have to be obtained separately.

• Delphi
• MSMS
• GROMACS

Usage

If MD DaVis is installed in a virtual environment, it should be activated before using MD DaVis. For example, to activate the virtual environment created with conda, use:

conda activate md_davis_env

The MD DaVis CLI can be called with:

md_davis

Author

Dibyajyoti Maity - www.djmaity.com