punkpony

topography_atlas_of_space

Code and instructions for making topographic maps of planets and moons

atomsk

Atomsk: A Tool For Manipulating And Converting Atomic Data Files -

InterMol

Conversion tool for molecular simulations

GromacsWrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

vpython-jupyter

3D visualization made easy

openpathsampling

An open source Python framework for transition interface and path sampling calculations.

pytim

a python package for the interfacial analysis of molecular simulations

ligpargen

conan

Analysis of contacts in molecular dynamics trajectories

matlab-novice-inflammation

Programming with MATLAB

OPLSAA-DB

Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.

SeaFreeze

The SeaFreeze package allows to compute the thermodynamic and elastic properties of water and ice polymorphs (Ih, III, V and VI) in the 0-2300 MPa and 220-500K range.

LSP-Grammarly

Grammarly support for Sublime's LSP plugin, using the Grammarly language server

jekyll-starter-kit

A simple framework for starting your own Jekyll project

MoloVol

MoloVol is a free, cross-plattform, scientific software for volume and surface computations of single molecules and crystallographic unit cells.

nap

Nagoya Atomistic-simulation Package (NAP). Why don't you take a NAP? ;)

ligpargen

A repository for tutorials and FAQ's about LigParGen

interfaceff2gro

A python script to prepare GROMACS input files using INTERFACE forcefield

atom

Atomistic Topology Operations in Matlab, scripts for manipulation of molecular dynamics or monte carlo simulation systems

FTMSVisualization

A suite of tools for visualizing complex mixture FT-MS data

RTIL-FF

Gromacs Topology Files for common Ionic Liquids

LigParGen_2.3

LigParGen python package version 2.3 (beta)

IR-Spectra

Code and examples to compute IR spectra from normal mode analysis

kimmdy

reactive MD python pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)

polypy

polygon (ring network) discovery from XYZ files

MKTOP

Automatic Construction of Molecular Topologies

pH-diagrams

A Python package to plot fractional composition diagrams and pH-log c diagrams

math-with-slack

Rendered math (MathJax) with Slack's desktop client (fork adds macro support)

nucleosynthesis

Clay-Project

Scripts for project