{"id":19021329,"url":"https://github.com/plumed/masterclass-2022","last_synced_at":"2026-04-28T14:30:21.574Z","repository":{"id":44013699,"uuid":"452613983","full_name":"plumed/masterclass-2022","owner":"plumed","description":null,"archived":false,"fork":false,"pushed_at":"2022-09-11T15:10:23.000Z","size":15,"stargazers_count":4,"open_issues_count":1,"forks_count":5,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-01-02T00:42:04.158Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"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}},"created_at":"2022-01-27T09:14:00.000Z","updated_at":"2024-11-22T14:11:33.000Z","dependencies_parsed_at":"2023-01-18T03:45:48.331Z","dependency_job_id":null,"html_url":"https://github.com/plumed/masterclass-2022","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%2Fmasterclass-2022","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/plumed%2Fmasterclass-2022/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/plumed%2Fmasterclass-2022/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/plumed%2Fmasterclass-2022/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/plumed","download_url":"https://codeload.github.com/plumed/masterclass-2022/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240065543,"owners_count":19742519,"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":"2024-11-08T20:21:17.468Z","updated_at":"2026-04-28T14:30:21.498Z","avatar_url":"https://github.com/plumed.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Masterclass 2022 - software\n\nIn this repository we report a brief guide on how to install the software needed for PLUMED Masterclass, 2022 series.\nNotice that different Masterclasses might require different software versions.\nOur recommendation is to use conda. Unfortunately we can only provide precompiled conda packages for x64 architecture, Linux and MacOS.\nThis means that if you want to run the exercise on a different architecture (e.g., a new Mac with a ARM processor) you should install the software on your own.\n\nFirst, make sure conda is installed by typing:\n```\nconda\n```\nIf the command is not found, please refer to these [instructions to install conda on your machine](https://docs.conda.io/en/latest/miniconda.html).\nAlternatively, if you use the [Homebrew package manager](https://brew.sh/), you can install conda with:\n```\nbrew install --cask anaconda\n# add this line to your .bashrc\nexport PATH=\"/usr/local/anaconda3/bin:$PATH\"\n```\n\nNow we can create a conda environment for the PLUMED Masterclass:\n```\nconda create --name plumed-masterclass-2022\n```\n\nand activate it with:\n```\nconda activate plumed-masterclass-2022\n```\n\nFinally, we can proceed with the installation of the required software:\n```\n# install some basic analysis tool and the default plumed version\nconda install -c conda-forge plumed py-plumed numpy pandas matplotlib notebook mdtraj mdanalysis git\n```\nIf the Masterclass requires Gromacs, you can then run the following command:\n```\n# install plumed 2.8.0 and gromacs 2020.6 with MPI and all modules enabled\nconda install --strict-channel-priority -c plumed/label/masterclass-2022 -c conda-forge plumed gromacs\n```\nIf the Masterclass requires LAMMPS instead (for instance, Masterclass 22.12), the appropriate command is:\n```\n# install plumed 2.8.0 and lammps 23 Jun 2022 with MPI and all modules enabled\nconda install --strict-channel-priority -c plumed/label/masterclass-2022 -c conda-forge plumed lammps\n```\nIf the Masterclass requires AMBER (for instance, Masterclass 22.13), you should first create a separate AMBER environment:\n```\n# create a separate AMBER environment and install AMBER\nconda create --name plumed-masterclass-2022-amber\nconda activate plumed-masterclass-2022-amber\nconda install -c conda-forge ambertools\n```\nAnd you should then stack the PLUMED and AMBER environments:\n```\n# stack the PLUMED and AMBER environments\nconda activate plumed-masterclass-2022\nconda activate --stack plumed-masterclass-2022-amber\nexport PLUMED_KERNEL=/your_path_here/plumed-masterclass-2022/lib/libplumedKernel.so\n```\n\nConda will install a number of packages.\nOn MacOS, for instance, you should see something similar to this:\n```\nThe following NEW packages will be INSTALLED:\n\n  boost-cpp          conda-forge/osx-64::boost-cpp-1.79.0-h8b082ac_0\n  gromacs            plumed/label/masterclass-2022/osx-64::gromacs-2020.6-h75233e6_1\n  icu                conda-forge/osx-64::icu-70.1-h96cf925_0\n  libhwloc           conda-forge/osx-64::libhwloc-1.11.13-hc10311c_0\n  libxml2            conda-forge/osx-64::libxml2-2.9.14-h08a9926_0\n  mpi                conda-forge/osx-64::mpi-1.0-openmpi\n  openmpi            conda-forge/osx-64::openmpi-4.1.3-hd33e60e_103\n\nThe following packages will be SUPERSEDED by a higher-priority channel:\n\n  plumed             conda-forge::plumed-2.8.0-nompi_h3651~ --\u003e plumed/label/masterclass-2022::plumed-2.8.0-h75233e6_1\n```\n Make sure that `gromacs` and `plumed` packages are installed from `plumed/label/masterclass-2022`.\n \n **Do not forget to activate the plumed-masterclass-2022 environment every time you open a new terminal/shell.**\n \n Notice that with some outdated conda version you might receive an error due to the fact that conda confuses python 3.1 with python 3.10.\n If you find an error like this one:\n ```\n PackagesNotFoundError: The following packages are not available from current channels:\n\n  - python=3.1\n\n ```\n Make sure that you have at least conda 4.11.0 (or update conda with `conda update conda`).\n More at [this link](https://github.com/conda/conda/issues/11065)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fplumed%2Fmasterclass-2022","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fplumed%2Fmasterclass-2022","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fplumed%2Fmasterclass-2022/lists"}