End-To-End Molecular Dynamics (MD) Engine using PyTorch

A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies

[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks

Generate coarse-grained molecular dynamics models from atomistic trajectories.

The source of the votca-csg and xtp packages

Example to fit parameters and run CG simulations using TorchMD and Schnet

COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3

Tools to build coarse grained models and perform simulations with OpenMM

COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM

SIRAH Force Field

Coarse-grained molecular dynamics simulation with the Single-Interaction-Site RNA model

NGAC

Tutorial to build a membrane with INSANE.

Use Case for the OpenModel project

Thesis repository on neural ordinary differential equations used for coarse-graining molecular dynamics

C++ package that provides tools for correcting structural predictions of proteins (eg. from X-Ray Crystallography or AlphaFold) using X-ray small-angle scattering (SAXS) in solution

Microstate Sparse Reconstruction (MSR): a backmapping method that recovers all-atom structures from reduced/coarse-grained variables

Predictive collective variable discovery with deep Bayesian models for atomistic systems.

A mesh free molecular dynamics (MD) simulation for a fluid in an isothermal container

A library for the Analysis of Molecular Dynamics Simulations of Self Assembling Peptides. Started during an internship at CNTE, Niguarda Hospital, Milan