{"id":19021295,"url":"https://github.com/plumed/conda","last_synced_at":"2025-04-23T07:31:31.189Z","repository":{"id":44441152,"uuid":"195082662","full_name":"plumed/conda","owner":"plumed","description":"Repository with conda recipes for LAMMPS, GROMACS, etc (WIP)","archived":false,"fork":false,"pushed_at":"2024-04-11T19:55:49.000Z","size":346,"stargazers_count":10,"open_issues_count":2,"forks_count":10,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-17T22:09:25.495Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/plumed.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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,"zenodo":null}},"created_at":"2019-07-03T15:35:23.000Z","updated_at":"2024-12-12T12:00:14.000Z","dependencies_parsed_at":"2024-04-03T08:30:33.213Z","dependency_job_id":"981f502a-8bce-4e09-ac54-e3b2ea9fa42e","html_url":"https://github.com/plumed/conda","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/plumed%2Fconda","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/plumed%2Fconda/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/plumed%2Fconda/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/plumed%2Fconda/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/plumed","download_url":"https://codeload.github.com/plumed/conda/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250391123,"owners_count":21422846,"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":[],"created_at":"2024-11-08T20:21:05.658Z","updated_at":"2025-04-23T07:31:31.165Z","avatar_url":"https://github.com/plumed.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Conda packages for GROMACS and LAMMPS\n\n## Install conda\n\nFirst you should install conda. In order to do so execute the commands below:\n\n````\nwget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh\n# on MacOS replace with:\n# wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh\nbash ./miniconda.sh -b -f -p /path/to/conda\nexport PATH=\"/path/to/conda/bin:$PATH\"\nsource activate base\n````\n\nHere `/path/to/conda` should be the path where you want to install conda. You can choose it in your home so that you will have write permission to it.\n\nYou might want to use a separate environment just for the Lugano tutorial. You can do it using the following commands\n\n````\nconda create --name lugano-tutorials\nsource activate lugano-tutorials\n````\n\nThe second command should be repeated every time you open a new shell.\nIn case you have already conda installed, by working in a separate environment you will make sure that there\nwill not be interference between packages specifically needed for this tutorial and packages that you have already installed.\n\n## Install PLUMED\n\nThis command installs a special version of PLUMED 2.5.1 that also includes the optional dimred module.\n\n````\nconda install -c plumed/label/lugano -c conda-forge plumed\n````\n\nMake sure you include the two channels in the right order, so that `plumed/label/lugano` has the priority, since the version\nof PLUMED available on conda-forge does not include the dimred module.\nOn OSX, the command above should install the following packages:\n\n````\n  gsl                conda-forge/osx-64::gsl-2.5-ha2d443c_0\n  libblas            conda-forge/osx-64::libblas-3.8.0-10_openblas\n  libcblas           conda-forge/osx-64::libcblas-3.8.0-10_openblas\n  libcxx             conda-forge/osx-64::libcxx-8.0.0-4\n  libcxxabi          conda-forge/osx-64::libcxxabi-8.0.0-4\n  libgfortran        conda-forge/osx-64::libgfortran-3.0.1-0\n  liblapack          conda-forge/osx-64::liblapack-3.8.0-10_openblas\n  libopenblas        conda-forge/osx-64::libopenblas-0.3.6-hd44dcd8_4\n  llvm-openmp        conda-forge/osx-64::llvm-openmp-8.0.0-h770b8ee_0\n  openblas           conda-forge/osx-64::openblas-0.3.6-hd44dcd8_4\n  plumed             plumed/label/lugano/osx-64::plumed-2.5.1-h0a44026_3\n  xdrfile            conda-forge/osx-64::xdrfile-1.1.4-h01d97ff_0\n  zlib               conda-forge/osx-64::zlib-1.2.11-h01d97ff_1005\n````\n\nAgain, notice that the `plumed` package comes from `plumed/label/lugano`, whereas all the libraries come from `conda-forge`.\n\n## Install GROMACS\n\nThis command installs a special version of GROMACS 2018.6 pre-patched with PLUMED.\nPatching is done in runtime mode, and should by default pick the PLUMED library installed\non conda in the same environment, using the command above. \n\n````\nconda install -c plumed/label/lugano -c conda-forge gromacs\n````\n\nOn OSX, the command above should install the following packages:\n\n````\n  fftw               conda-forge/osx-64::fftw-3.3.8-mpi_mpich_h6e18f22_1006\n  gromacs            plumed/label/lugano/osx-64::gromacs-2018.6-h2b26ce3_0\n  icu                conda-forge/osx-64::icu-58.2-h0a44026_1000\n  libhwloc           conda-forge/osx-64::libhwloc-1.11.9-0\n  libiconv           conda-forge/osx-64::libiconv-1.15-h01d97ff_1005\n  libxml2            conda-forge/osx-64::libxml2-2.9.9-hd80cff7_1\n  mpi                conda-forge/osx-64::mpi-1.0-mpich\n  mpich              conda-forge/osx-64::mpich-3.2.1-ha90c164_1013\n  xz                 conda-forge/osx-64::xz-5.2.4-h1de35cc_1001\n````\n\nNotice that MPI is installed as a requirement of one of the libraries used by GROMACS, but GROMACS itself\nwill be installed in non-MPI version (with openMP parallelism enabled).\n\n\n## Install LAMMPS\n\nThis command installs a special version of LAMMPS 2019, June, pre-patched with PLUMED.\nPatching is done in runtime mode, and should by default pick the PLUMED library installed\non conda in the same environment, using the command above. \n\n````\nconda install -c plumed/label/lugano -c conda-forge lammps\n````\n\nOn OSX, the command above should install the following packages:\n\n````\n  lammps             plumed/label/lugano/osx-64::lammps-2019.6.5-h2b26ce3_0\n  libjpeg-turbo      conda-forge/osx-64::libjpeg-turbo-2.0.2-h1de35cc_0\n  libpng             conda-forge/osx-64::libpng-1.6.37-h2573ce8_0\n````\n\n## Install other software that you will need\n\nUsing conda you might also install other software that will be used during the workshop.\nYou will likely need these python packages:\n\n````\nconda install -c conda-forge numpy\nconda install -c conda-forge scipy\n````\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fplumed%2Fconda","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fplumed%2Fconda","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fplumed%2Fconda/lists"}