MDAnalysis

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM’s powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X.


References in zbMATH (referenced in 9 articles )

Showing results 1 to 9 of 9.
Sorted by year (citations)

  1. Adam R. Symington: polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories (2021) not zbMATH
  2. Luciano G. Silvestri, Lucas J. Stanek, Gautham Dharuman, Yongjun Choi, Michael S. Murillo: Sarkas: A Fast Pure-Python Molecular Dynamics Suite for Plasma Physics (2021) arXiv
  3. T. L. Underwood, J. A. Purton, J. R. H. Manning, A. V. Brukhno, K. Stratford, T. Düren, N. B. Wilding, S. C. Parker: dlmontepython: A Python library for automation and analysis of Monte Carlo molecular simulations (2021) arXiv
  4. Barrett, R.; Chakraborty, M.; Amirkulova, D.; Gandhi, H.; Wellawatte, G.; White, A.: HOOMD-TF: GPU-Accelerated, Online Machine Learning in the HOOMD-blue Molecular Dynamics Engine (2020) not zbMATH
  5. Nicolas Renaud; Cunliang Geng: The pdb2sql Python Package: Parsing, Manipulation and Analysis of PDB Files Using SQL Queries (2020) not zbMATH
  6. Teixeira, J. M.: taurenmd: A command-line interface for analysis of Molecular Dynamics simulations (2020) not zbMATH
  7. Andrew Abi-Mansour: PyGran: An object-oriented library for DEM simulation and analysis (2019) not zbMATH
  8. Bercin, Kutalmis M.; Xie, Zheng-Tong; Turnock, Stephen R.: Exploration of digital-filter and forward-stepwise synthetic turbulence generators and an improvement for their skewness-kurtosis (2018)
  9. Michaud-Agrawal, Naveen; Denning, Elizabeth J.; Woolf, Thomas B.; Beckstein, Oliver: Mdanalysis: A toolkit for the analysis of molecular dynamics simulations (2011) ioport