gmx-install

Automate GROMACS source installation with PLUMED patching and CUDA/MPI configuration.

1|1|Updated Apr 16, 2026

Search Tags:#benchmarking #gpu #installation #cuda #mpi #gromacs #plumed

Ready to run

npx skills add https://github.com/BioKT/Skills-BIOKT --skill gmx-install

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: gmx-install
Source: https://github.com/BioKT/Skills-BIOKT/tree/main/gmx-install
Command: npx skills add https://github.com/BioKT/Skills-BIOKT --skill gmx-install

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

GROMACS source installation, patching with PLUMED, and enabling GPU and MPI support is complex and time-consuming; this skill automates the end-to-end workflow to simplify setup and validation, including optional benchmarking.

Core Features & Use Cases

End-to-end GROMACS from-source installation with PLUMED integration
GPU offload enabled via CUDA and MPI support for scalable HPC runs
Benchmarking and validation steps to verify a correct, performant build
Use Case: reinstalling or updating GROMACS on HPC clusters with patching and performance checks

Quick Start

Run the six-step workflow to install GROMACS from source with PLUMED, enabling GPU, MPI, and optional benchmarking.

Frequently Asked Questions about gmx-install

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I install GROMACS from source with PLUMED, GPU, and MPI support?▼

To install GROMACS from source with PLUMED, GPU, and MPI, follow a six-step workflow: set install paths, build PLUMED, patch GROMACS, configure with CMake, build and install, and run optional benchmarks.

What versions of GROMACS and PLUMED are used for source installation and patching?▼

The source installation and PLUMED patching workflow uses default GROMACS version 2024.2 and PLUMED version 2.9.2, automating the end-to-end build process for GPU and MPI configurations.

Do I need CUDA and MPI to configure GROMACS for scalable HPC runs?▼

Yes, you need CUDA for GPU offload and MPI for scalable HPC runs to configure GROMACS. Compilers, MPI, and CUDA are required prerequisites before building and installing the patched source.

Can I run performance benchmarks after building GROMACS from source with PLUMED?▼

Yes, you can run performance benchmarks after building GROMACS from source with PLUMED. The workflow includes optional benchmarking and validation steps to verify a correct and performant build.

What's the best way to update GROMACS on an HPC cluster with PLUMED patching and performance checks?▼

The best way to update GROMACS on an HPC cluster with PLUMED patching is to automate the six-step workflow, which handles CMake configuration, source patching, and performance benchmarking checks.

Why does patching GROMACS with PLUMED for GPU and MPI take so much time to set up?▼

Patching GROMACS with PLUMED for GPU and MPI is complex because it requires setting install paths, building PLUMED, applying the patch, and configuring CMake with correct CUDA and MPI options before installation.