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pynamd

Python Tools for NAMD

pysfd

pytorch_tutorial

《Pytorch模型训练实用教程》中配套代码

radical.ensemblemd

The Radical Ensemble Molecular Dynamics (MD) Toolkit

remd

repex

Python replica-exchange simulation facility for OpenMM.

ring-open-fep

Ring-opening strategy for FEP.

screenlamp

screenlamp is a Python toolkit for hypothesis-driven virtual screening

scriptmd

Useful scripts for MD simulation and analysis

scripts

Various Python packages and programs

scripts-1

Compilation of different scripts used for my MD analysis

seminario

Tool to compute bond and angle force field parameters with the Seminario method

simanalysistools

Tools to analyze output of molecular simulations

stitch

Utility for parameterizing ligands with CHARMM36 CGenFF

testing-1

Collection of scripts

timber

Package to simplify setup of TI free energy calculations with AMBER.

toolbx_pdb

Tools to manipulate and execute tasks on a protein complex ensemble

toolbx_vs

Tools to setup, monitor and analyse a virtual screening on HPC clusters.

ttclust

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)

ugatit

Official Tensorflow implementation of U-GAT-IT: Unsupervised Generative Attentional Networks with Adaptive Layer-Instance Normalization for Image-to-Image Translation

v2ray.fun

A easily command interaction manager for v2ray

vermouth-martinize

Describe and apply transformation on molecular structures and topologies

watermd

westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

workers-proxy

Lightweight JavaScript reverse proxy built with Cloudflare Workers.

zhihu-oauth

尝试解析出知乎官方未开放的 OAuth2 接口，并提供优雅的使用方式，作为 zhihu-py3 项目的替代者，目前还在实验阶段