Molecular dynamics allows the atoms and molecules to interact for a fixed period of time, giving a view of the dynamic “evolution” of the system.
MDAnalysis is a Python library to analyze molecular dynamics simulations.
RadonPy is a Python library to automate physical property calculations for polymer informatics.
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
An open source Python framework for transition interface and path sampling calculations.
Fully automated high-throughput MD pipeline
PyRod - Tracing water molecules in molecular dynamics simulations
Automated omics-scale protein modeling and simulation setup.
Full automation of relative protein-ligand binding free energy calculations in GROMACS
blend molecules!
MDAnalysis tool to calculate membrane curvature.
a logistics and persistence engine for the analysis of molecular dynamics trajectories
pKa estimates for proteins using an ensemble approach
Sparse Gaussian Process Potentials
To analyze fluctuations in DNA or RNA structures in molecular dynamics trajectories.
A codebase for classical molecular dynamics (MD) simulation setup and results analysis.
Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.
Code for the paper LaM-SLidE - Latent Space Modeling of Spatial Dynamical Systems via Linked Entities
A repository for tutorials and FAQ's about LigParGen