coarse-grained-molecular-dynamics
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End-To-End Molecular Dynamics (MD) Engine using PyTorch
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Jan 16, 2025 - Python
A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
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Mar 18, 2025 - Python
[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks
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Aug 26, 2023 - Python
Generate coarse-grained molecular dynamics models from atomistic trajectories.
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Dec 8, 2022 - Python
The source of the votca-csg and xtp packages
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Jan 20, 2025 - C++
Example to fit parameters and run CG simulations using TorchMD and Schnet
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Feb 4, 2022 - Jupyter Notebook
COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
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Feb 24, 2025 - Jupyter Notebook
Tools to build coarse grained models and perform simulations with OpenMM
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Dec 16, 2022 - Python
COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM
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Dec 2, 2023 - Python
SIRAH Force Field
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Dec 13, 2024
Coarse-grained molecular dynamics simulation with the Single-Interaction-Site RNA model
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Mar 12, 2025 - Fortran
NGAC
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Jul 5, 2019
Tutorial to build a membrane with INSANE.
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Jan 31, 2018 - Makefile
Use Case for the OpenModel project
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Dec 13, 2024 - Perl
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
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Sep 20, 2024 - C++
Microstate Sparse Reconstruction (MSR): a backmapping method that recovers all-atom structures from reduced/coarse-grained variables
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Mar 14, 2021 - C++
A mesh free molecular dynamics (MD) simulation for a fluid in an isothermal container
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May 31, 2020 - C++
Predictive collective variable discovery with deep Bayesian models for atomistic systems.
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Oct 23, 2020 - Python
A library for the Analysis of Molecular Dynamics Simulations of Self Assembling Peptides. Started during an internship at CNTE, Niguarda Hospital, Milan
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Jul 30, 2023 - Jupyter Notebook
Thesis repository on neural ordinary differential equations used for coarse-graining molecular dynamics
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Dec 30, 2022 - Python
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