{"id":19339531,"url":"https://github.com/becksteinlab/conda-gromacs-2016","last_synced_at":"2026-05-18T05:02:00.049Z","repository":{"id":137557823,"uuid":"68867030","full_name":"Becksteinlab/conda-gromacs-2016","owner":"Becksteinlab","description":"Conda package of gromacs 2016 intended for testing purposes. ","archived":false,"fork":false,"pushed_at":"2017-02-28T00:18:33.000Z","size":6,"stargazers_count":0,"open_issues_count":3,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-06T10:48:27.997Z","etag":null,"topics":["conda","gromacs"],"latest_commit_sha":null,"homepage":"","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Becksteinlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-09-21T23:48:53.000Z","updated_at":"2017-02-28T00:22:32.000Z","dependencies_parsed_at":null,"dependency_job_id":"0acbb433-bcbf-48ac-a551-743681120646","html_url":"https://github.com/Becksteinlab/conda-gromacs-2016","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fconda-gromacs-2016","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fconda-gromacs-2016/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fconda-gromacs-2016/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fconda-gromacs-2016/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Becksteinlab","download_url":"https://codeload.github.com/Becksteinlab/conda-gromacs-2016/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240442541,"owners_count":19801917,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["conda","gromacs"],"created_at":"2024-11-10T03:22:42.897Z","updated_at":"2026-05-18T05:01:55.021Z","avatar_url":"https://github.com/Becksteinlab.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# README for conda-gromacs-2016\n\nThis repository contains everything needed to build\n[conda](https://conda.io/docs/) packages for the popular\n[Gromacs](http://www.gromacs.org) molecular dynamics package.\n\n**WARNING**: The package builds a **minimal, portable Gromacs version** that is\nprimarily useful for testing. It is **not recommended to use it for\nproduction-scale simulations.**\n\nReduced performance features:\n* only thread parallelization\n* uses bundled FFT (not a fast FFT)\n* no GPU support\n\n\n## Using the installed package\n\nMultiple versions of Gromacs can be installed in parallel. A script\n`get_gmx` is installed in the user's home directory that allows the\nuser to select the desired version of Gromacs. It returns the path to\nthe `GMXRC` startup script, which in turn needs to be sourced to set\nup the Gromacs environment. For instance, to select version\n*2016* one would run in the shell\n\n```\nsource `get_gmx 2016`\n```\n\n\n## Pre-built packages\nAnaconda packages for *linux-64* are available in the Anaconda Cloud channel\n[anaconda.org/becksteinlab](https://anaconda.org/becksteinlab). If you\nhave `conda` installed you can install this package with\n\n```\nconda install -c becksteinlab gromacs-2016\n```\n\n## Building the package\nIt is recommended to build the package within a minimal docker container. \nBuild the docker container by invoking\n\n```\ndocker build -t gmx_build .\n```\nin the same directory as the provided Dockerfile.\n\nStart the docker container with `docker run -it gmx_build`. If everything \nworks as expected, then you should find yourself in an environment similar\nto:\n\n```\n[root@0f6a75177395 /]# \n```\n\nNavigate to `/root/gromacs` to find the build scripts. Run: \n\n```\nbash build_conda_package.sh\n```\n\nOnce this has finished move to the parent directory to find your package in tar.bz2 \narchive.\n\n### Keep locally or push to cloud:\n\n#### Copy to host machine\nFrom a new terminal find the container ID with `docker ps`. With this ID, invoke:\n\n```\ndocker cp \u003cCONTAINER ID\u003e:/root/\u003cCONDA_TAR_BZ2\u003e $OUTPUT_DIR\n```\n\nYou should be able to find the conda package in the output directory.\n\nTo exit the docker container type `exit`.\n\n#### Upload directly to Anaconda cloud\n\nTo upload directly to a the Anaconda clound through your Anaconda username, run:\n```\nanaconda upload -u \u003cANACONDA USERNAME\u003e \u003cCONDA_TAR_BZ2\u003e\n```\n\nTo exit the docker container type `exit`\n\n## Licensing\n\n[Gromacs](http://www.gromacs.org/About_Gromacs) itself is published\nunder the GNU\n[Lesser General Public License](http://www.gnu.org/licenses/lgpl-2.1.html)\n(LGPL), version 2.1. The files to *build anaconda packages* are\nlicensed under the MIT license (see file `LICENSE`).\n\n\n## Contributing\n\nWe welcome contributions in the form of issue reports and pull requests.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fconda-gromacs-2016","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecksteinlab%2Fconda-gromacs-2016","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fconda-gromacs-2016/lists"}