Software for automated molecular dynamics studies
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Updated
Aug 6, 2026 - Python
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md-analysis
Here are 6 public repositories matching this topic...
Molecular dynamics pre- and post-processing toolkit.
python cheminformatics clustering structural-biology molecular-dynamics pytorch openmm computational-chemistry pca tica rdkit numba free-energy gromacs trajectory-analysis mdtraj cupy jax md-analysis openfe
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Jul 30, 2026 - Python
MD-permeation: a FORTRAN code to analyze MD simulation trajectories and identify permeation events for water molecules.
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Mar 2, 2022 - Fortran
sbm-tools is a simple python package for creating, modifying, and maintaining input files for native Structure-Based Model simulations to be used with the popular simulation software GROMACS.
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Mar 11, 2020 - Python
GROMOS++ Software for the Analysis of (Bio)molecular Simulation Trajectories
trajectory-analysis biomolecular-simulation md-analysis md-trajectory simulation-analysis gromos gromos-software gromosplspls molecular-simulation-analysis
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Aug 19, 2025 - C++
Conformational dynamics, dPCA, K-Means, FEL, DCCM, MMGBSA & virtual screening analysis of AMR enzyme ANT(3″)-Ia from A. baumannii and S. aureus | Python · MDAnalysis · Schrödinger · Scikit-learn · Amber
python machine-learning bioinformatics scikit-learn computational-biology molecular-dynamics-simulation principal-component-analysis virtual-screening mmgbsa kmeans-clustering-algorithm molecular-docking antimicrobial-resistance md-analysis admet computional-chemistry silhouette-analysis dynamic-cross-correlation-matrx free-energy-landscape admet-prediction
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Aug 3, 2026 - HTML
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