Open source library to work with molecular systems
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Updated
May 21, 2024 - Python
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.
Open source library to work with molecular systems
This repo contains python scripts used in Mack et al. 2022 (doi.org/10.1016/j.jmb.2022.167482). This includes MD simulations code and analysis scripts. The usage of these Python scripts is further explained in the enclosed readme file
Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics.
MDAnalysis is a Python library to analyze molecular dynamics simulations.
Real time molecular dynamics in the browser using LAMMPS
Graphics Processing Units Molecular Dynamics
mirrored from https://gitlab.com/ccp5/dl-poly/
The Website of the Ramiréz Lab
Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbor lists, etc.
ls1-MarDyn is a massively parallel Molecular Dynamics (MD) code for large systems. Its main target is the simulation of thermodynamics and nanofluidics. ls1-MarDyn is designed with a focus on performance and easy extensibility.
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
LAMMPS tutorials for both beginners and advanced users
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
Wrapping GROMACS by python script for me
Tools for Analyzing and Debugging (SA)FEP calculations. See also the SAFEP Tutorial: https://github.com/jhenin/SAFEP_tutorial/tree/main Documentation: https://safep-alchemy.readthedocs.io/en/latest/
ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations
SAPT energy calculator built using MDAnalysis and Psi4
Sample codes for my book on molecular dynamics simulation