taf-gromacs

TAFFISH wrapper for GROMACS, a molecular dynamics simulation and analysis suite for biomolecules, polymers, liquids, and other molecular systems.

This TAFFISH app packages GROMACS 2026.2 as a CPU-only container build and exposes the upstream gmx command through the versioned taf-gromacs wrapper.

Release 2026.2-r2 is a help-only TAFFISH update. It keeps the upstream software, Dockerfile, runtime dependencies, smoke tests, and command behavior unchanged from 2026.2-r1, and refreshes the terminal taf-gromacs --help text.

Build Profile

This release is intentionally a portable baseline build:

GROMACS version: 2026.2
precision: mixed / single
parallelism: thread-MPI + OpenMP
GPU support: off
external MPI: off
FFT library: FFTW3 single precision
SIMD: None / portable scalar
PLUMED interface: enabled in gmx mdrun; no standalone PLUMED package

The goal is to provide a reliable default app for system preparation, small to medium CPU simulations, and trajectory analysis. It intentionally avoids CPU-specific SIMD assumptions; users who need maximum performance should build a site-local SIMD/GPU/MPI tuned variant. GPU, CUDA-aware MPI, SYCL, OpenCL, HIP, NVSHMEM, and external-MPI cluster builds are important GROMACS configurations, but they are hardware and site dependent. Those should be handled by a separate TAFFISH app variant, a site-local image, or explicit runtime policy rather than being hidden inside this baseline image.

Installation

Install from the public TAFFISH Hub index:

taf update
taf install gromacs

Install the exact release:

taf install gromacs 2026.2-r2

For local testing before publication:

taf install --from .

Usage

Show TAFFISH app help:

taf-gromacs --help

Show the TAFFISH package version:

taf-gromacs --version

Show upstream GROMACS version information:

taf-gromacs gmx --version

List upstream commands:

taf-gromacs gmx help commands

Show help for a specific GROMACS command:

taf-gromacs gmx mdrun -h
taf-gromacs gmx grompp -h
taf-gromacs gmx pdb2gmx -h

Because this app uses TAFFISH command mode, the first non-option argument is treated as the command to run inside the container. Since GROMACS itself is subcommand-driven, the clearest and recommended form is:

taf-gromacs gmx <gromacs-subcommand> [options...]

For example:

taf-gromacs gmx pdb2gmx -f protein.pdb -o processed.gro -p topol.top
taf-gromacs gmx editconf -f processed.gro -o boxed.gro -c -d 1.0 -bt cubic
taf-gromacs gmx solvate -cp boxed.gro -cs spc216.gro -o solvated.gro -p topol.top
taf-gromacs gmx grompp -f minim.mdp -c solvated.gro -p topol.top -o em.tpr
taf-gromacs gmx mdrun -deffnm em -ntmpi 1 -ntomp 4
taf-gromacs gmx trjconv -s md.tpr -f md.xtc -o centered.xtc

Do not write taf-gromacs mdrun ... for normal use. In command mode, mdrun would be interpreted as an executable inside the container, not as a subcommand of gmx.

For option-leading arguments to the default gmx command, use --:

taf-gromacs -- --version
taf-gromacs -- -h

Included Functionality

The image includes the upstream gmx executable, GROMACS shared libraries, the standard GROMACS data directory, and built-in force-field/topology data under /opt/gromacs/share/gromacs.

Common command groups include:

system preparation:  pdb2gmx, editconf, solvate, genion, make_ndx
run input:           grompp, convert-tpr
simulation:          mdrun
trajectory tools:    trjconv, trjcat, trjorder, check
analysis tools:      energy, rms, rmsf, gyrate, hbond, distance, rdf, sasa
format/report tools: dump, report-methods, xpm2ps

Use taf-gromacs gmx help commands for the full command list for this build. gmx mdrun -h also exposes the upstream -plumed option in this build, but the image does not package a separate plumed executable or a custom PLUMED-patched GROMACS variant.

Boundaries

This baseline app does not include:

CUDA, SYCL, HIP, OpenCL, or other GPU acceleration
external MPI or GPU-aware MPI
NVSHMEM or cuFFTMp
standalone PLUMED tooling or custom PLUMED-patched GROMACS variants
gmxapi / nblib developer API packaging
third-party analysis suites such as MDAnalysis, VMD, MDTraj, or PyMOL

These are not missing hidden runtime dependencies for the standard gmx command. They are alternate build modes, site-specific accelerator stacks, or separate tools that should be composed explicitly.

High-Performance Needs

Use this release when you want a portable GROMACS environment for preparation, analysis, teaching, testing, or modest CPU-only runs. For long production MD simulations, GPU acceleration and hardware-tuned builds are often important.

Users with high-performance needs should either build GROMACS from the official instructions for their own hardware or watch for future TAFFISH variants that may target specific accelerator stacks, for example:

gromacs-cuda   NVIDIA CUDA builds
gromacs-hip    AMD ROCm/HIP builds
gromacs-sycl   Intel/AMD SYCL builds
gromacs-mpi    external-MPI or cluster-oriented builds

Those variants are intentionally not folded into taf-gromacs because one GROMACS build can only target one GPU backend, and accelerator/MPI stacks depend on drivers, compilers, cluster policy, and the target hardware. A site-local image built from the official GROMACS documentation may be the best option for production HPC environments.

Package

name: gromacs
command: taf-gromacs
version: 2026.2-r2
kind: tool
image: ghcr.io/taffish/gromacs:2026.2-r2

Container

The container is built from docker/Dockerfile. It starts from debian:13-slim, downloads the official gromacs-2026.2.tar.gz source archive, verifies its SHA256 checksum, compiles with CMake and Ninja, installs to /opt/gromacs, and keeps only runtime libraries in the final image.

The image is intended for native:

linux/amd64
linux/arm64

The smoke metadata checks:

exist: gmx
test:  gmx reports version 2026.2
test:  command list and mdrun help are available
test:  editconf converts a minimal GRO file to PDB
test:  grompp builds a tiny water TPR and mdrun runs a zero-step simulation

Smoke tests validate installation, force-field data access, basic file conversion, run-input generation, and a minimal CPU mdrun path. They do not replace scientific validation of molecular dynamics protocols.

Upstream

• Homepage: https://www.gromacs.org/
• Source and releases: https://gitlab.com/gromacs/gromacs
• Public GitHub mirror: https://github.com/gromacs/gromacs
• Documentation: https://manual.gromacs.org/2026.2/
• Download: https://ftp.gromacs.org/gromacs/gromacs-2026.2.tar.gz
• License: LGPL-2.1-or-later
• Software DOI: 10.5281/zenodo.20037885
• Related citation: Abraham et al. 2015, doi:10.1016/j.softx.2015.06.001