{"id":37617649,"url":"https://github.com/bio-phys/cnt-martini","last_synced_at":"2026-01-16T10:33:32.814Z","repository":{"id":29009301,"uuid":"119984726","full_name":"bio-phys/cnt-martini","owner":"bio-phys","description":"Generates Martini models for open carbon nanotubes to use with Gromacs.","archived":false,"fork":false,"pushed_at":"2021-11-24T01:39:12.000Z","size":108,"stargazers_count":15,"open_issues_count":1,"forks_count":4,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-09-09T19:36:19.758Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/bio-phys.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}},"created_at":"2018-02-02T13:26:05.000Z","updated_at":"2025-04-04T11:52:43.000Z","dependencies_parsed_at":"2022-07-26T07:17:19.874Z","dependency_job_id":null,"html_url":"https://github.com/bio-phys/cnt-martini","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bio-phys/cnt-martini","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fcnt-martini","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fcnt-martini/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fcnt-martini/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fcnt-martini/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bio-phys","download_url":"https://codeload.github.com/bio-phys/cnt-martini/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fcnt-martini/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478050,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2026-01-16T10:33:32.361Z","updated_at":"2026-01-16T10:33:32.804Z","avatar_url":"https://github.com/bio-phys.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Open Carbon Nanotubes for the Martini Model\n\nGenerates a Martini model for an open carbon nanotube (CNT) for use with the Gromacs simulation package.\nIt provides a structure file (.gro), a topology-include file (.itp) and a position-restraints file (.itp).\n\nTools to analyze Martini CNT simulations can be found here: https://github.com/bio-phys/cnt-martini-analysis. \n\n## Requirements\n\nPython (2/3) with packages argparse, math, and sys\n\n## Usage\n\nFor a new nanotube model, run \n\n    python martini-cnt-generator.py -nr [number of rings] \\\n                                    -rs [number of beads per ring] \\\n                                    -bl [bond length] \\\n                                    -bf [bond force const.] \\\n                                    -af [angle force const.] \\\n                                    -bt [bead type] \\\n                                    -ft [bead type of the functional groups] \\\n                                    -fb [number of functionalized rings at one end] \\\n                                    -fe [number of functionalized rings at the other end] \\\n                                    --base36\n\nfor example\n\n    python martini-cnt-generator.py -nr 12 -rs 8 -bl 0.47 -bt CNP -ft SNda -fb 1 -fe 1\n\nAll arguments are optional. If an argument is not used, the default value for the standard CNT porin [1] is used.\n\n## Notes\n\n* By default, atom names are a letter denoting their function (C - plain carbon grid, F - funcional group) plus the last three digits of their atom number (decimal system). The flag `--base36` switches to a base of 36 (including letters) to expand the number of unique atom names from 10^3 = 1000 (decimal) to 36^3 = 46656.\n* For large CNTs, a higher force constant than the standard value of 5000 should be used. A rule of thumb is to use a value of 20000 if the circumference exceeds 10 beads/ring or the length exceeds 15 rings. \n* The script produces position restraints, too. These are usually inteded for equilibration. They will not work with a Parrinello-Rahman barostat. \n\n## Literature\n\nIf the script or the model is helpful, please cite:\n- [1]  M. Vögele, J. Köfinger, G. Hummer: \n    Simulations of Carbon Nanotube Porins in Lipid Bilayers.\n    Faraday Discuss., 2018, 209, 341-358, DOI: 10.1039/C8FD00011E  \n    http://pubs.rsc.org/en/content/articlelanding/2018/fd/c8fd00011e\n\nThe model is based on previous work:\n- [2] R. M. Bhaskara, S. M. Linker, M. Vögele, J. Köfinger, G. Hummer \n    Carbon Nanotubes Mediate Fusion of Lipid Vesicles.\n    ACS Nano, 2017, 11 (2), pp 1273–1280\n- [3] M. Vögele, G. Hummer:\n    Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes.\n    J. Phys. Chem. B, 2016, 120 (33), pp 8722–8732\n    DOI: 10.1021/acs.jpcb.6b05102\n- [4] S. Baoukina, L. Monticelli, D.P. Tieleman:\n    Interaction of Pristine and Functionalized Carbon Nanotubes with Lipid Membranes. \n    J. Phys. Chem. B (2013), 117, 12113-23.\n- [5] L. Monticelli\n    On atomistic and coarse-grained models for C60 fullerene. \n    J. Chem. Theory Comput. (2012), 8, 1370−1378 (DOI: 10.1021/ct3000102). \n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio-phys%2Fcnt-martini","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbio-phys%2Fcnt-martini","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio-phys%2Fcnt-martini/lists"}