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:

2025.3-0

depends _openmp_mutex:

>=4.5

depends fftw:

>=3.3.10,<4.0a0

depends libgcc:

>=13

depends libhwloc:

2.*

depends libhwloc:

>=2.12.1,<2.12.2.0a0

depends libstdcxx:

>=13

depends ocl-icd:

>=2.3.3,<3.0a0

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install gromacs_mddb

and update with::

   mamba update gromacs_mddb

To create a new environment, run:

mamba create --name myenvname gromacs_mddb

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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