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amber_tutorials Public
Some tutorials on how to use AMBER simulation package. Especially for Amber22+AmberTools23.
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MindSPONGE Public
Classic Molecular Dynamics with MindSPONGE
Apache License 2.0 UpdatedJul 16, 2025 -
FEP-SPell-ABFE-benchmark Public
This repo contains some scripts and data information for FEP-SPell-ABFE-benchmark.
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AI2BMD Public
Forked from microsoft/AI2BMDAI-powered ab initio biomolecular dynamics simulation
Python MIT License UpdatedFeb 18, 2025 -
FEP-SPell-ABFE Public
FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery
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ErrorBP-NN Public
Implement the error backpropagation algorithm for neural network.
Jupyter Notebook MIT License UpdatedNov 22, 2024 -
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KL-Divergence Public
Understanding Kullback–Leibler-Divergence (also called relative entropy and I-divergence) intuitively by a constructive approach to measuring distribution differences.
UpdatedNov 21, 2024 -
alphafold3 Public
Forked from google-deepmind/alphafold3AlphaFold 3 inference pipeline.
Python Other UpdatedNov 11, 2024 -
manim Public
Forked from ManimCommunity/manimA community-maintained Python framework for creating mathematical animations.
Python MIT License UpdatedSep 23, 2024 -
LennardJonesFluid Public
An example defining alchemically-modified potentials using OpenMM
Python MIT License UpdatedJul 10, 2024 -
vim-plug Public
Forked from junegunn/vim-plug🌺 Minimalist Vim Plugin Manager
Vim Script MIT License UpdatedJul 9, 2024 -
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a3fe Public
Forked from michellab/a3feAutomated Adaptive Absolute alchemical Free Energy calculator
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tfep Public
Forked from andrrizzi/tfepA library to perform targeted free energy perturbation with normalizing flows.
Python MIT License UpdatedJun 5, 2024 -
LaTeX-OCR Public
Forked from lukas-blecher/LaTeX-OCRpix2tex: Using a ViT to convert images of equations into LaTeX code.
Python MIT License UpdatedJun 5, 2024 -
colvars Public
Forked from Colvars/colvarsCollective variables library for molecular simulation and analysis programs
C++ GNU Lesser General Public License v3.0 UpdatedMay 28, 2024 -
vermouth-martinize Public
Forked from marrink-lab/vermouth-martinizeDescribe and apply transformation on molecular structures and topologies
Python Apache License 2.0 UpdatedMay 1, 2024 -
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pycuda Public
Forked from inducer/pycudaCUDA integration for Python, plus shiny features
Python Other UpdatedNov 10, 2023 -
free_energy_papers Public
To summarize the key points in papers about (alchemical) free energy simulations and calculations
1 UpdatedNov 9, 2023 -
mbar_wham Public
Multistate Bennett Acceptance Ratio & Weighted Histogram Analysis Method
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articlesWeChat Public
This repo is used to hold some public files and scripts on WeChat articles
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udlbook Public
Forked from udlbook/udlbookUnderstanding Deep Learning - Simon J.D. Prince
Jupyter Notebook Other UpdatedOct 17, 2023 -
openmm Public
Forked from openmm/openmmOpenMM is a toolkit for molecular simulation using high performance GPU code.
C++ UpdatedOct 16, 2023