{"id":16694466,"url":"https://github.com/ricalessandri/polyp3ht","last_synced_at":"2025-03-13T23:23:31.506Z","repository":{"id":89870011,"uuid":"125734706","full_name":"ricalessandri/PolyP3HT","owner":"ricalessandri","description":"Polymerize Atomistic P3HT","archived":false,"fork":false,"pushed_at":"2020-06-06T16:51:34.000Z","size":59,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-20T18:42:27.858Z","etag":null,"topics":["atomistic","force-fields","molecular-dynamics","polymers"],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ricalessandri.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}},"created_at":"2018-03-18T14:43:13.000Z","updated_at":"2020-06-06T16:51:36.000Z","dependencies_parsed_at":"2023-03-06T10:30:15.691Z","dependency_job_id":null,"html_url":"https://github.com/ricalessandri/PolyP3HT","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/ricalessandri%2FPolyP3HT","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ricalessandri%2FPolyP3HT/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ricalessandri%2FPolyP3HT/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ricalessandri%2FPolyP3HT/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ricalessandri","download_url":"https://codeload.github.com/ricalessandri/PolyP3HT/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243495821,"owners_count":20299993,"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":["atomistic","force-fields","molecular-dynamics","polymers"],"created_at":"2024-10-12T16:46:03.292Z","updated_at":"2025-03-13T23:23:31.486Z","avatar_url":"https://github.com/ricalessandri.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PolyP3HT : Polymerize Atomistic P3HT\n\nHandy script to generate topology and geometry files of arbitrarily long atomistic P3HT chains.\n\nTwo force fields are available:\n\n1. The GROMOS 53A6-based parameters published in \n[JACS **2017**, *139*, 3697-3705](https://pubs.acs.org/doi/abs/10.1021/jacs.6b11717) - see the **`2017RA-JACS`** folder; \n\n2. The \"Q-Forced\" parameters (still relying on the GROMOS 53A6 Lennard-Jones parameters) published\nin [Chemrxiv **2020**](https://doi.org/10.26434/chemrxiv.12277931) - see the **`2020RA-qforce`** folder.\nThis version improves the bonded parameters of P3HT, which were otherwise too flexible \nwith the GROMOS standard parameters for angles and improper dihedrals in particular. \nThis model is *recommended for use in combination with subsequent quantum chemical calculations* \non the P3HT geometries (see, *e.g*, [Chemrxiv **2020**](https://doi.org/10.26434/chemrxiv.12277931)).\n\nBoth can be also downloaded from [Figshare](http://doi.org/10.6084/m9.figshare.5853060), \nwhich contains also a few example files obtained with the scripts.\n\"Stable\" releases will be uploaded to [Figshare](http://doi.org/10.6084/m9.figshare.5853060),\nwhile this repo is a good place where to raise issues or make improvements.\n\n\n## Use\n\n```\ncd 2017RA-JACS\n./PolyP3HT.sh       12   # on Linux\n./PolyP3HT-macOS.sh 12   # on macOS\n```\n\nwhere 12 is the desired number of monomers (note only that the number of monomers in the chain *must* \nbe a multiple of 2). \nNote that the files `shift-resnr.py`, `residuetypes.dat`, `p3ht_dimer_repeat_unit_50atoms.gro`, `header`, \nand `top2itp.sh` must be in the folder where the script is being exectured along with the directory \n`p3ht_gromos_v_2017RA-JACS.ff/` which contains the force field.\nThe commands are analogous for the `2020RA-qforce` version. \nThe output files are in GROMACS format (`itp` and `gro` for the topology and geometry, respectively).\nMore details are also included in the Supporting Information of [Chemrxiv **2020**](https://doi.org/10.26434/chemrxiv.12277931).\n\n\n## License\n\n\u003cpre\u003e\u003ccode\u003e\nCopyright 2018 University of Groningen\n\nLicensed under the Apache License, Version 2.0 (the \"License\");\nyou may not use this file except in compliance with the License.\nYou may obtain a copy of the License at\n\n      http://www.apache.org/licenses/LICENSE-2.0\n\nUnless required by applicable law or agreed to in writing, software\ndistributed under the License is distributed on an \"AS IS\" BASIS,\nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\nSee the License for the specific language governing permissions and\nlimitations under the License.\n\u003c/code\u003e\u003c/pre\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fricalessandri%2Fpolyp3ht","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fricalessandri%2Fpolyp3ht","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fricalessandri%2Fpolyp3ht/lists"}