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 ≥ 3.9

Installation

The easiest installation method is with Anaconda or Miniconda. Create a conda environment called md-davis with all required dependencies using the following command:

conda env create djmaity/md-davis

Activate the environment with:

conda activate md-davis

Install MD DaVis in this environment using:

pip install md-davis

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

Dependencies

The following tools required for full functionality will have to be obtained separately.

• Delphi v8.1 or later
• DSSP v2.3.0
• MSMS v2.6.1
• GROMACS v5.1.4 or later

Usage

Remember to activate the md-davis environment before using MD DaVis.

conda activate md-davis

The MD DaVis graphical user interface can be invoked with:

md-davis-gui

The MD DaVis command line tool can be called with:

md-davis

The MD DaVis package can be used in a Python script with a standard import statement like:

import md_davis

Author

Dibyajyoti Maity - www.djmaity.com