Starred repositories
A comprehensive pipeline for analyzing molecular dynamics trajectories and generating high-quality Gibbs Free Energy Surface visualizations using GROMACS and Python. Features automated PCA analysis…
Updated xpm2txt.py to be compatible with Python 3.10
KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
Martini 3 Building Blocks for Lipid Nanoparticle Design
A Python-based tool to automatically generate LAMMPS configurations and input files for polymer-solvent systems with optional crosslinking and crowding effects.
Stochastically modelling the crosslinking reaction between polymers
Xlink is a Python script that uses Gromacs to automatically perfom simulation crosslinking and generate atomistic model of aromatic polyamide membrane separation layer. Currently it can use trimesi…
Generate polymer crosslinking network under gromacs enviroment
python simulation interface for molecular modeling
这是一个基于AutoDock-GPU的自动化批量对接程序，只需输入小分子的smiles结构文档（支持批量输入）并且提供蛋白质的网格文件（maps.fld）即可自动完成小分子预处理，分子对接，结果提取等步骤。This project is an automated batch docking pipeline built on AutoDock-GPU, designed to streaml…
Field Theoretic Simulation (FTS) code to study Liquid-Liquid Phase Separation (LLPS) in model IDPs.
code to perform coarse-grained simulations of RNA liquid-liquid phase separation
A small program helps finding water bridge in pdb files, written in fortran. Please note that it's a first usable version, and only support CHARMM-formatted PDB file.
Hydrogen bonding networks from electronegativity atom (X=O, N, S) to other electronegativity atoms via water (solvent) bridge.
A simple tool for creating and running MD simulations, using Jupyter and OpenMM
LAMMPS Membrane Builder for n-phase biomembrane systems
Calculate the buried surface area of ligands in the protein-ligand complex.
Little scripts and functions to make my work with VMD easier
VMD Tcl language scripts of molecular dynamics modeling, analyzing, and visualization.
Some of useful tcl scripts to analyse data from VMD