coarse-grained-molecular-dynamics 开源项目推荐（41 个）

torchmd /torchmd

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

jewettaij /moltemplate

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

kyonofx /mlcgmd

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

jag1g13 /pycgtool

Generate coarse-grained molecular dynamics models from atomistic trajectories.

votca /votca

The source of the votca-csg and xtp packages

MikkelDA /COBY

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

torchmd /torchmd-cg

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

PanosAntoniadis /platito

PLaTITO is an open-source model for generative molecular dynamics of proteins.

shirtsgroup /cg_openmm

Tools to build coarse grained models and perform simulations with OpenMM

mosdef-hub /msibi

A package for deriving coarse-grain potentials using MultiState Iterative Boltzmann Inversion (MS-IBI)

vuqv /cosmo

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

SIRAHFF /documentation

SIRAH Force Field

msidore /tutorial_insane

Tutorial to build a membrane with INSANE.

Hori-Lab /UNISIS

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

kdwykleingeld /ngac

NGAC

martincalvelo /MARTINI-CG-TUTORIALS

Repository of tutorials on Coarse-Grained Molecular Dynamics (CG-MD) using the Martini 3 force field, designed for running on Google Colab

Prior-Lab-Durham-University /carbonara

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

anabiman /msr

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

jakublala /coarsegrained-md-neural-ode

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

hothello /openmodel

Use Case for the OpenModel project