End-To-End Molecular Dynamics (MD) Engine using PyTorch
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Updated
Oct 10, 2024 - Python
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
Tools to build coarse grained models and perform simulations with OpenMM
COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM
SIRAH Force Field
NGAC
Coarse-grained molecular dynamics simulation with the Single-Interaction-Site RNA model
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
Predictive collective variable discovery with deep Bayesian models for atomistic systems.
Use Case for the OpenModel project
Tutorial to build a membrane with INSANE.
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
Thesis repository on neural ordinary differential equations used for coarse-graining molecular dynamics
Microstate Sparse Reconstruction (MSR): a backmapping method that recovers all-atom structures from reduced/coarse-grained variables
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