Package Recipe 'gromacs_mddb'

recipe gromacs_mddb

GROMACS is a versatile package to perform molecular dynamics.

Homepage:: https://www.gromacs.org/
Documentation:: https://manual.gromacs.org/
Developer docs:: https://gitlab.com/gromacs/gromacs/-/tree/pj_mddb_json_proto-2025
License:: LGPL / LGPL-2.1-or-later
Recipe:: /gromacs_mddb/meta.yaml

Development version of GROMACS in colaboration to MDDB to add the possibility to export tpr to json.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

package gromacs_mddb¶

Versions:

2025.3-3, 2025.3-2, 2025.3-1, 2025.3-0

Depends:

on _openmp_mutex >=4.5
on fftw >=3.3.10,<4.0a0
on libgcc >=13
on libhwloc <2.12.2
on libhwloc >=2.12.1,<2.12.2.0a0
on libstdcxx >=13
on ocl-icd >=2.3.3,<3.0a0

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install gromacs_mddb

to add into an existing workspace instead, run:

pixi add gromacs_mddb

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install gromacs_mddb

Alternatively, to install into a new environment, run:

conda create -n envname gromacs_mddb

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/gromacs_mddb:<tag>

(see gromacs_mddb/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/gromacs_mddb/README.html)