Overview
DynamiSpectra: from molecular dynamics simulations to comprehensive data analysis
DynamiSpectra is an advanced Python package designed for analyzing molecular dynamics simulation data. Built to process and interpret results primarily from GROMACS https://www.gromacs.org/ structure, DynamiSpectra provides a streamlined and efficient workflow for researchers in the field of molecular dynamics. By leveraging the power of Python, this package enables users to perform complex analyses, visualize molecular behaviors, and gain valuable insights from simulation outputs. Whether you’re studying protein folding, ligand interactions, or other molecular phenomena, DynamiSpectra empowers you to dive deep into your data and uncover meaningful patterns.
It provides powerful tools to calculate and visualize a wide range of molecular properties, including Hydrogen bonds, Root Mean Square Deviation, Root Mean Square Fluctuation, Solvent Accessible Surface Area, Radius of Gyration, Secondary Structure Analysis, and Principal component. These features enable researchers to gain deep insights into the dynamics of molecular systems, study conformational changes, and investigate interactions between molecules with greater precision.
Installation
pip install DynamiSpectra
You can also install the in-development version with:
pip install https://github.com/Conradoou/DynamiSpectra/archive/main.zip
Note: DynamiSpectra uses the package SciPy, which requires a fortran compiler to be installed to build its source,which can be tricky on some systems. An alternative to this is to use Anaconda environment. DynamiSpectra can then be more easily installed within this environment, using the command line or preferred method. Installing DynamiSpectra may take some time on certain systems. If you observe the command line halting, please be patient, as the installation process may require seconds to minutes to complete.
Documentation
Demo
In the repository, specifically in DynamiSpectra/datas, there are several folders for each analysis with the corresponding GROMACS output data for testing.