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2021-10-20-febs-gromacs-tutorial

GROMACS introduction tutorial for FEBS workshop

autodocking-utils

Docker implementation of autodocking, openbabel, rdkit and lots of molecular dynamics utilities.

bio_python

Python based bio and md analysis setup

biolab_preparation

How to start biolab with Anaconda, Jupyter, streamlit, gromacs, ambertools etc.

containers

Bioinformatics containers

docker_tf_gro

dockernel

Dockerized Jupyter kernels.

gmx_template

This is a template/example of MD simulations using Gromacs

gmxapi-tutorials

Python examples and tutorial material for gmxapi 0.3 on GROMACS 2022

gnina

A deep learning framework for molecular docking

gromacs

backup repo for doing experiments with GROMACS on SC20 virtual student cluster competition

gromacs-docker

Dockerfile for GROMACS

gromacs-hpccm-recipes-mult-stages

HPCCM recipes for GROMACS container

gromacs-workshop-installation

Installation instructions for Gromacs workshops

gromacs_py

Gromacs_py is a python library allowing a simplified use of the gromacs MD simulation software. Gromacs_py can build topologie based on a pdb file, create the simulation system (box, add water and ions) and run minimisation, equilibration and production run.

gromacswrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2021 supported).

jupyter_dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

jupyter_dock_devel

md-silver-nps

molecular-dyamics-protein-in-water

A tutorial to run molecular dynamics (protein in water) with Gromacs

molecular_dynamics_utils

ngl

WebGL protein viewer

pyvol

volume calculation and segmentation

react-ngl

React wrapper for ngl

s1a35_ti_citrate

scripts_notebooks

xvg-plotter

XVG Plotter is a plotting tool for xvg files based on streamlit library.