Deprecated Package: biobb_md is no longer maintained and has been superseded by the biobb_gromacs package. Biobb_md is the Biobb module collection to perform molecular dynamics simulations.
Biobb_md is the Biobb module collection to perform molecular dynamics simulations. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.
Important: PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY.
pip install "biobb_md>=3.7.2"
Usage: Python API documentation
conda install -c bioconda "biobb_md>=3.7.2"
Usage: With conda installation BioBBs can be used with the Python API documentation and the Command Line documentation
docker pull quay.io/biocontainers/biobb_md:3.7.2--pyhdfd78af_0
docker run quay.io/biocontainers/biobb_md:3.7.2--pyhdfd78af_0 <command>
MacOS users: it's strongly recommended to avoid Singularity and use Docker as containerization system.
singularity pull --name biobb_md.sif shub://bioexcel/biobb_md
singularity exec biobb_md.sif <command>
The command list and specification can be found at the Command Line documentation.
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).
- (c) 2015-2021 Barcelona Supercomputing Center
- (c) 2015-2021 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
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