A tool for comparative analysis of molecular dynamics simulations of proteins.
Project description
MD DaVis
Introduction
MD DaVis is a tool for comparative analysis of molecular dynamics simulations of proteins.
Documentation: https://md-davis.readthedocs.io
Features
- Free energy landscape
- Residue properties plot
- Surface electrostatics
- Electric field dynamics
- 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.
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
Project details
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