{"id":15048566,"url":"https://github.com/jerkwin/gmxtools","last_synced_at":"2025-04-05T13:04:41.737Z","repository":{"id":44459332,"uuid":"204320104","full_name":"Jerkwin/gmxtools","owner":"Jerkwin","description":"tools for GROMACS","archived":false,"fork":false,"pushed_at":"2025-03-26T07:35:38.000Z","size":52935,"stargazers_count":107,"open_issues_count":3,"forks_count":52,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-05T13:04:00.096Z","etag":null,"topics":["gromacs","md","simulaton"],"latest_commit_sha":null,"homepage":"https://jerkwin.github.io/gmxtools/","language":"HTML","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/Jerkwin.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}},"created_at":"2019-08-25T16:24:58.000Z","updated_at":"2025-03-29T22:58:03.000Z","dependencies_parsed_at":"2024-12-22T17:24:41.019Z","dependency_job_id":null,"html_url":"https://github.com/Jerkwin/gmxtools","commit_stats":{"total_commits":129,"total_committers":1,"mean_commits":129.0,"dds":0.0,"last_synced_commit":"1ad9cc236bb3bfeb858118a278c053a3c4513742"},"previous_names":["jerkwin/gmxtool"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jerkwin%2Fgmxtools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jerkwin%2Fgmxtools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jerkwin%2Fgmxtools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jerkwin%2Fgmxtools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Jerkwin","download_url":"https://codeload.github.com/Jerkwin/gmxtools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247339154,"owners_count":20923014,"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":["gromacs","md","simulaton"],"created_at":"2024-09-24T21:14:04.347Z","updated_at":"2025-04-05T13:04:41.705Z","avatar_url":"https://github.com/Jerkwin.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cbody\u003e\u003cdiv class=\"wrapper\"\u003e\n\t\u003cheader\u003e\n\t\t\u003ch1\u003e\u003ca href=\"https://jerkwin.github.io/gmxtools/\"\u003egmxtools\u003c/a\u003e\u003c/h1\u003e\n\t\t\u003cp\u003escripts/programs/utilities/tools for GROMACS\u003c/p\u003e\n\t\t\u003cp class=\"view\"\u003e\u003ca href=\"#Introduction\"\u003eIntroduction\u003c/a\u003e\u003c/p\u003e\n\t\t\u003cp class=\"view\"\u003e\u003ca href=\"#Tools\"\u003eTools\u003c/a\u003e\u003c/p\u003e\n\t\u003c/header\u003e\n\n\u003ch2 id=\"Introduction\"\u003eIntroduction\u003c/h2\u003e\n\n\u003cp\u003eThis is a collection of the tools I used for GROMACS. Hope it helps for you as well.\u003c/p\u003e\n\u003cp\u003eIf you use one/some of the tools for your publication(s), I will appreciate if you cite the Zenodo DOI \u003ca href=\"https://doi.org/10.5281/zenodo.6408973\"\u003e10.5281/zenodo.6408973\u003c/a\u003e\u003c/p\u003e\n\n\u003ch2 id=\"Tools\"\u003eTools\u003c/h2\u003e\u003c/p\u003e\n\n\u003ctable\u003e\n\u003cth\u003e名称\u003cbr\u003eNAME\u003c/th\u003e\u003cth\u003e说明\u003cbr\u003eINSTRUCTION\u003c/th\u003e \u003cth\u003e代码\u003cbr\u003eCODE\u003c/th\u003e \u003cth\u003e示例\u003cbr\u003eEXAMPLE\u003c/th\u003e\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003ecalc\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://jerkwin.github.io/2019/11/19/%E5%9C%A8%E7%BA%BF%E8%AE%A1%E7%AE%97%E5%85%BC%E5%8D%95%E4%BD%8D%E6%8D%A2%E7%AE%97%E5%99%A8/\"\u003e在线计算兼单位换算器\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./calc/calc.html\"\u003ecalc\u003c/a\u003e\u003cbr\u003e\n\u003ca 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href=\"https://jerkwin.github.io/2018/08/29/Pi-Pi%E5%A0%86%E7%A7%AF%E8%B7%9D%E7%A6%BB%E5%92%8C%E5%A0%86%E7%A7%AF%E8%A7%92%E5%BA%A6%E7%9A%84%E8%AE%A1%E7%AE%97/\"\u003ePi-Pi堆积距离和堆积角度的计算\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./pipistack/pipistack.tcl\"\u003epipistack.tcl\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"./pipistack/pipistack_linalg.tcl\"\u003epipistack_linalg.tcl\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./pipistack/ph2.zip\"\u003eph2.zip\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003expm2all\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://jerkwin.github.io/2018/05/09/xpm%E6%96%87%E4%BB%B6%E5%A4%84%E7%90%86%E8%84%9A%E6%9C%AC/\"\u003expm文件处理脚本\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"https://jerkwin.github.io/2020/02/29/%E5%88%86%E5%AD%90%E6%A8%A1%E6%8B%9F%E5%91%A8%E5%88%8A-%E7%AC%AC_8_%E6%9C%9F/\"\u003expm2all: 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颜色方案\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"https://jerkwin.github.io/2024/01/14/dssp%E6%95%B0%E6%8D%AE%E7%BB%98%E5%9B%BE%E8%84%9A%E6%9C%ACdssp2gp/\"\u003edssp数据绘图脚本dssp2gp\u003c/a\u003e\n\n\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./dssp2gp/dssp2gp.bsh\"\u003edssp2gp.bsh\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./dssp2gp/ss.xpm\"\u003edssp.dat\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003egmx_mmpbsa\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\n\u003ca href=\"https://jerkwin.github.io/2019/07/31/gmx_mmpbsa%E4%BD%BF%E7%94%A8%E8%AF%B4%E6%98%8E/\"\u003egmx_mmpbsa使用说明\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"https://jerkwin.github.io/2021/03/16/gmx_mmpbsa%E8%84%9A%E6%9C%AC%E6%9B%B4%E6%96%B0-%E5%B1%8F%E8%94%BD%E6%95%88%E5%BA%94%E4%B8%8E%E7%86%B5%E8%B4%A1%E7%8C%AE/\"\u003egmx_mmpbsa脚本更新：屏蔽效应与熵贡献\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"https://jerkwin.github.io/2021/11/26/gmx_mmpbsa%E8%84%9A%E6%9C%AC%E6%9B%B4%E6%96%B0-%E6%B8%85%E7%90%86%E6%95%B4%E7%90%86%E8%BE%93%E5%87%BA/\"\u003egmx_mmpbsa脚本更新：清理整理输出\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"https://jerkwin.github.io/2022/02/09/gmx_mmpbsa%E6%9B%B4%E6%96%B0-%E4%BF%AE%E6%AD%A3%E5%8E%9F%E5%AD%90%E5%8D%8A%E5%BE%84bug,_%E6%94%B9%E7%94%A8AMBRR_PB4,_%E4%B8%99%E6%B0%A8%E9%85%B8%E6%89%AB%E6%8F%8FCAS/\"\u003egmx_mmpbsa更新：修正原子半径bug, 改用AMBRR PB4, 丙氨酸扫描CAS\u003c/a\u003e\n\n\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./gmx_mmpbsa/gmx_mmpbsa.bsh\"\u003egmx_mmpbsa.bsh\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./gmx_mmpbsa/1ebz.zip\"\u003e1ebz.zip\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003egmx_ir\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://jerkwin.github.io/2017/08/20/%E4%BD%BF%E7%94%A8GROMACS%E8%AE%A1%E7%AE%97%E7%BA%A2%E5%A4%96%E5%85%89%E8%B0%B1/\"\u003e使用GROMACS计算红外光谱\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"https://jerkwin.github.io/2024/04/08/trr%E8%BD%A8%E8%BF%B9%E8%BD%AC%E6%8D%A2%E7%A8%8B%E5%BA%8Ftrr2all/\"\u003etrr轨迹转换程序trr2all\u003c/a\u003e\n\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./gmx_ir/gmx_ir.bsh\"\u003egmx_ir.bsh\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003etrr2all\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://jerkwin.github.io/2017/08/20/%E4%BD%BF%E7%94%A8GROMACS%E8%AE%A1%E7%AE%97%E7%BA%A2%E5%A4%96%E5%85%89%E8%B0%B1/\"\u003e使用GROMACS计算红外光谱\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"https://jerkwin.github.io/2024/04/08/trr%E8%BD%A8%E8%BF%B9%E8%BD%AC%E6%8D%A2%E7%A8%8B%E5%BA%8Ftrr2all/\"\u003etrr轨迹转换程序trr2all\u003c/a\u003e\n\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./trr2all/trr2all.exe\"\u003etrr2all.exe\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./trr2all/spc216.zip\"\u003espc216.zip\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003egmx_hbdat\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\n\u003ca href=\"https://jerkwin.github.io/2021/06/19/GROMACS氢键分析工具hbond的使用及扩展/\"\u003eGROMACS氢键分析工具hbond的使用及扩展\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"https://jerkwin.github.io/2022/05/23/使用gnuplot绘制氢键数据的平行轴图/\"\u003e使用gnuplot绘制氢键数据的平行轴图\u003c/a\u003e\u003cbr\u003e\n\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./gmx_hbdat/gmx_hbdat.bsh\"\u003egmx_hbdat.bsh\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./gmx_hbdat/hbdat_1crn.zip\"\u003ehbdat_1crn.zip\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003eremd_tgenerator\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://jerkwin.github.io/2021/09/30/副本交换动力学T-REMD模拟的温度分布计算器/\"\u003e副本交换动力学T-REMD模拟的温度分布计算器\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./remd_tgenerator/remd_tgenerator.html\"\u003eremd_tgenerator\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003exff\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://jerkwin.github.io/2022/04/15/%E5%8A%9B%E5%9C%BA%E6%8B%9F%E5%90%88%E5%B7%A5%E5%85%B7xff%E5%BC%80%E5%8F%91%E6%9D%82%E8%AE%B0/\"\u003e力场拟合工具xff开发杂记\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./xff/xff.html\"\u003exff\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./xff/c6h6.fchk\"\u003ec6h6.fchk\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"./xff/sf6.FChk\"\u003esf6.FChk\u003c/a\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003ecagen\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://jerkwin.github.io/2022/09/02/%E6%B0%B4%E6%BA%B6%E6%B6%B2%E4%BD%93%E7%B3%BB%E6%88%90%E7%AC%BC%E5%88%86%E6%9E%90%E7%A8%8B%E5%BA%8Fcagen/\"\u003e水溶液体系成笼分析程序cagen\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./cagen/cagen.zip\"\u003ecagen.zip\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003efitmol\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./fitmol/README.md.html\"\u003eREADME\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./fitmol/FitMol.f90\"\u003eFitMol.f90\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./fitmol/ch4.xyz\"\u003ech4.xyz\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"./fitmol/ch4_ch3oh.xyz\"\u003ech4_ch3oh.xyz\u003c/a\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\n\u003ctr\u003e\n\u003ctd\u003e\u003ccode\u003ematchmol\u003c/code\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://jerkwin.github.io/2023/06/02/%E5%88%86%E5%AD%90%E7%BB%93%E6%9E%84%E5%8C%B9%E9%85%8D%E7%A8%8B%E5%BA%8Fmatchmol/\"\u003e分子结构匹配程序matchmol\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"./matchmol/matchmol.zip\"\u003ematchmol.zip\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\n\u003c/table\u003e\n\n\u003ch2 id=\"Questions\"\u003eQuestions?\u003c/h2\u003e\u003c/p\u003e\n\nIf you have any quesiotns about these tools, please let me know.\n\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://groups.google.com/forum/#!forum/gmxtools\"\u003eGoogle Forum\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/Jerkwin/gmxtools/issues\"\u003eGitHub issues\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/div\u003e\u003c/body\u003e","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjerkwin%2Fgmxtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjerkwin%2Fgmxtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjerkwin%2Fgmxtools/lists"}