Instructions for how to package VMD for Ubuntu and not pull your hair out in the process.

Robinhood Policy Engine : a versatile tool to monitor filesystem contents and schedule actions on filesystem entries.

Scalable cluster administration Python framework — Manage node sets, node groups and execute commands on cluster nodes in parallel.

"rsync for cloud storage" - Google Drive, S3, Dropbox, Backblaze B2, One Drive, Swift, Hubic, Wasabi, Google Cloud Storage, Azure Blob, Azure Files, Yandex Files

Slurm: A Highly Scalable Workload Manager

Tools for Analyzing and Debugging (SA)FEP calculations. See also the SAFEP Tutorial: https://github.com/jhenin/SAFEP_tutorial/tree/main Documentation: https://safep-alchemy.readthedocs.io/en/latest/

ZFS Automatic Snapshot Service for Linux

Collective variables library for molecular simulation and analysis programs

Biomolecular simulation trajectory/data analysis.

Singularity definition files for development and maintenance of the EncoMPASS database. Does not contain any scientific software: only Linux packages or libraries needed for their installation.

Pairwise alignment of membrane protein sequences

A generative model for programmable protein design

Fast PBC wrapping and unwrapping for VMD

A collection of tools for characterizing membrane structure and dynamics within simulated trajectories of molecular systems.

HDXer is a package to compute Hydrogen-Deuterium exchange data from biomolecular simulations, compare to experiment, and perform ensemble refinement to fit a structrual ensemble to the experimental…

OpenZFS on Linux and FreeBSD

Colvars-patched GROMACS releases; CI disabled until it is fixed in standard GROMACS

Example files for Colvars module: https://github.com/Colvars/colvars

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

Windows Secure Shell Client With Support For Smart Cards, Certificates, & FIDO Keys

Rocky Linux is a community enterprise Operating System designed to be 100% bug-for-bug compatible with Enterprise Linux created in response to the effective discontinuation of CentOS.

Clone of the main LAMMPS repository containing an updated Colvars module.

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

Open source smart card tools and middleware. PKCS#11/MiniDriver

Tool to build force field input files for molecular simulation

A library of optimized math functions targeted at 32-bit and 64-bit x86 Linux systems

oneAPI DPC++ Library (oneDPL) https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/dpc-library.html

Installable VMD as a python module

Mobile Shell

MDAnalysis is a Python library to analyze molecular dynamics simulations.