RiesBen

ExampleNotebooks

Notebooks demonstrating how to do simple tasks related to free energy calculations.

openfe

The Open Free Energy toolkit

jGBM-Homepage

PyGromosTools

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

reffix

This is a small repository for my personal bibtex file managment.

thesis_free_energy_methods

This project contains all latex files and repo hooks, that I used to write my PhD dissertation! The template was passed on by generations of PhDs. Thanks to DHahn for passing it to me.

Ensembler

Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method development or to deepen understanding of a broad spectrum of modeling methods, from basic sampling techniques to enhanced sampling and free energy calculations. It is easy to install, fast, increases shareability, comparability, and reproducibility of scientific code developments.

restraintmaker

Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation technique with coordinate-based particles). It can be used on a script layer or as an interactive plugin for PyMol. Features are different selection modes and Optimizers to distribute restraints.

RiesBen/thesis_free_energy_methods

This project contains all latex files and repo hooks, that I used to write my PhD dissertation! The template was passed on by generations of PhDs. Thanks to DHahn for passing it to me.

RiesBen/jGBM-Homepage

RiesBen/PyGromosTools

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

RiesBen/reffix

This is a small repository for my personal bibtex file managment.

RiesBen/ABFE_workflow

RiesBen/BioinformaticsI-Assigments

RiesBen/polyHack2021_SBB

Here are our results for the SBB challenge on polyHack2021, which made the 3rd Price in the contest! Convenient traveling with SBB to your outdoor activity of choice? Use this tool to get the best and most convenient trips to your activity of choice. You can get inspired or plan with us! This project is a concept idea generated in 24 hours, and therefore not all functionality might work.

RiesBen/reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

RiesBen/DASH-tree

Partial Charge assignment for Molecular Dynamics

RiesBen/Ensembler

fast and easy development of simulation methods and teaching purposes

RiesBen/gromosPlsPls

RiesBen/gromosXX

md++ code

RiesBen/IndustryBenchmarks2024

Repository for the 2024 OpenFE industry benchmark efforts

RiesBen/kartograf-feedstock

A conda-smithy repository for kartograf.

RiesBen/Memorare

this is a suprise

RiesBen/openfreeenergy.github.io

RiesBen/openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

RiesBen/openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

RiesBen/PyGromacs

RiesBen/pylattica

A simple framework for prototyping lattice evolution simulations e.g. cellular automata, lattice gas simulations, lattice Monte Carlo etc.

RiesBen/qm.md

Source of the homepage qm.md

RiesBen/restraintmaker

RiesBen/RiesBen.github.io

this is my short resume

RiesBen/scikit-mol

scikit-learn classes for molecular vectorization using RDKit

RiesBen/swarmer

RiesBen/vsCNN

A C++ and Python implementation of the volume-scaled common nearest neighbor clustering algorithm