{"id":346,"date":"2016-10-17T15:44:46","date_gmt":"2016-10-17T06:44:46","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/?page_id=346"},"modified":"2026-04-13T12:45:56","modified_gmt":"2026-04-13T03:45:56","slug":"memo","status":"publish","type":"page","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/","title":{"rendered":"\u30e1\u30e2"},"content":{"rendered":"\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2025\/06\/26\/conformational-search-of-small-molecules-using-gromacs\/\" title=\"Conformational Search of Small Molecules Using GROMACS\">\u4f4e\u5206\u5b50\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u63a2\u7d22<\/a> (GROMACS, simulated annealing)<\/li>\n\n\n\n<li><a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/docking-simulation\/\" data-type=\"page\" data-id=\"403\">\u30bf\u30f3\u30d1\u30af\u8cea-\u30ea\u30ac\u30f3\u30c9\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3<\/a> (AutoDock)<\/li>\n\n\n\n<li><a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/md-simulation\/\" data-type=\"page\">C1\u30c9\u30e1\u30a4\u30f3\u306eGROMACS\u7528\u30c8\u30dd\u30ed\u30b8\u30fc\u751f\u6210<\/a> (AmberTools, Acpype)<\/li>\n\n\n\n<li><a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/md-simulation\/protein-ligand-complex\/\">\u30bf\u30f3\u30d1\u30af\u8cea-\u30ea\u30ac\u30f3\u30c9\u8907\u5408\u4f53\u306eMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3<\/a> (GROMACS)<\/li>\n\n\n\n<li><a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2020\/02\/06\/%e3%83%af%e3%83%bc%e3%82%af%e3%82%b9%e3%83%86%e3%83%bc%e3%82%b7%e3%83%a7%e3%83%b3%e5%b0%8e%e5%85%a5%e3%81%ae%e8%a8%98%e9%8c%b2%e3%80%81feb-6-2020-%e3%80%82\/\" data-type=\"post\" data-id=\"1931\">\u30ef\u30fc\u30af\u30b9\u30c6\u30fc\u30b7\u30e7\u30f3\u5c0e\u5165\u306e\u8a18\u9332\u3001Feb. 6\u201317, 2020\u3002<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/%e3%83%af%e3%83%bc%e3%82%af%e3%82%b9%e3%83%86%e3%83%bc%e3%82%b7%e3%83%a7%e3%83%b3%e6%97%a7%e7%92%b0%e5%a2%83%e3%81%ae%e8%a8%98%e9%8c%b2%ef%bc%88centos-7%ef%bc%89\/\" title=\"\u30ef\u30fc\u30af\u30b9\u30c6\u30fc\u30b7\u30e7\u30f3\u65e7\u74b0\u5883\u306e\u8a18\u9332\uff08CentOS 7\uff09\">\u65e7OS\u74b0\u5883\u306e\u8a18\u9332\uff08CentOS 7; until Aug. 2025\uff09<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/softwares\/\">\u8a08\u7b97\u7528\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\uff08Mac OS X\/macOS\u3001\u60c5\u5831\u304c\u53e4\u3044\uff09<\/a><\/li>\n<\/ul>\n\n\n\n<p><strong><a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/workstation\/\" title=\"Workstation\">\u5185\u90e8\u5c02\u7528\u30da\u30fc\u30b8: \u8a08\u7b97\u6a5f\u5229\u7528\u306e\u624b\u5f15\u304d<\/a><\/strong><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u30d1\u30c3\u30b1\u30fc\u30b8\u30d7\u30ed\u30b0\u30e9\u30e0\u4e00\u89a7<\/h2>\n\n\n\n<p>\uff082026\u5e744\u670813\u65e5\u66f4\u65b0\uff09<\/p>\n\n\n\n<p>AlmaLinux 8.10\uff082025\u5e748\u670820\u65e5\u5c0e\u5165\uff09<\/p>\n\n\n\n<figure class=\"wp-block-table is-style-stripes\"><table><thead><tr><th>\u540d\u524d<\/th><th>\u5185\u5bb9<\/th><\/tr><\/thead><tbody><tr><td><a href=\"https:\/\/ambermd.org\/AmberMD.php\" title=\"\">Amber<\/a> &amp; <a href=\"https:\/\/ambermd.org\/AmberTools.php\">AmberTools<\/a><\/td><td>\u5206\u5b50\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u30d7\u30ed\u30b0\u30e9\u30e0\u30d1\u30c3\u30b1\u30fc\u30b8<\/td><\/tr><tr><td><a href=\"https:\/\/ccsb.scripps.edu\/mgltools\/\" title=\"\">AutoDock<\/a><\/td><td>\u81ea\u52d5\u30c9\u30c3\u30ad\u30f3\u30b0\u30c4\u30fc\u30eb\u30b9\u30a4\u30fc\u30c8<\/td><\/tr><tr><td><a href=\"http:\/\/www.gromacs.org\/\">GROMACS<\/a><\/td><td>\u5206\u5b50\u52d5\u529b\u5b66 (MD) \u30d7\u30ed\u30b0\u30e9\u30e0\u30d1\u30c3\u30b1\u30fc\u30b8<\/td><\/tr><tr><td><a href=\"http:\/\/openmopac.net\/\">MOPAC<\/a><\/td><td>\u534a\u7d4c\u9a13\u7684\u5206\u5b50\u8ecc\u9053\u7406\u8ad6\u8a08\u7b97<\/td><\/tr><tr><td><a href=\"https:\/\/orcaforum.kofo.mpg.de\/app.php\/portal\">ORCA<\/a><\/td><td>ab initio\u91cf\u5b50\u5316\u5b66\u8a08\u7b97<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<figure class=\"wp-block-table is-style-stripes\"><table><thead><tr><th>\u30d1\u30c3\u30b1\u30fc\u30b8\u30d7\u30ed\u30b0\u30e9\u30e0\u540d<\/th><th>\u30d0\u30fc\u30b8\u30e7\u30f3<\/th><th>\u30ea\u30d3\u30b8\u30e7\u30f3<\/th><th>\u30b3\u30de\u30f3\u30c9<\/th><th>\u5c0e\u5165\/\u66f4\u65b0\u65e5<\/th><th>\u5099\u8003<\/th><\/tr><\/thead><tbody><tr><td>AmberTools &amp; pmemd<\/td><td>25<\/td><td>update.3 &amp; update.3<\/td><td>&nbsp;<\/td><td>2026\/04\/13<\/td><td><a href=\"https:\/\/ccportal.ims.ac.jp\/node\/3841\" title=\"\">from source<\/a><\/td><\/tr><tr><td>AutoDock-GPU<\/td><td>4.2.6<\/td><td>&nbsp;<\/td><td>&nbsp;<\/td><td>2025\/08\/20<\/td><td>&nbsp;<\/td><\/tr><tr><td>CP2K<\/td><td>2026.1<\/td><td><\/td><td>cp2k.psmp<\/td><td>2026\/04\/10<\/td><td><\/td><\/tr><tr><td>GROMACS<\/td><td>2026.1<\/td><td><\/td><td>gmx, gmx_mpi_d_cp2k<\/td><td>2026\/04\/10<\/td><td>CUDA 12.8, PyTorch 2.7.1<br>Torch-ani<\/td><\/tr><tr><td><\/td><td>2026.0<\/td><td><\/td><td>gmx<\/td><td>2026\/02\/13<\/td><td>CUDA 12.8, PyTorch 2.7.1<br>Torch-ani<\/td><\/tr><tr><td><\/td><td>2025.4<\/td><td><\/td><td>gmx<\/td><td>2025\/12\/05<\/td><td>CUDA 12.8, PyTorch 2.7.1<br>Torch-ani<\/td><\/tr><tr><td><\/td><td>2025.3<\/td><td>&nbsp;<\/td><td>gmx<\/td><td>2025\/09\/01<\/td><td>CUDA 12.8, PyTorch 2.7.1<br>Torch-ani<\/td><\/tr><tr><td><\/td><td>2025.2<\/td><td><\/td><td>gmx<\/td><td>2025\/08\/20<\/td><td>CUDA 12.9.1<\/td><\/tr><tr><td>MOPAC<\/td><td>23.1.2<\/td><td><\/td><td>mopac<\/td><td>2025\/07\/11<\/td><td><\/td><\/tr><tr><td>ORCA<\/td><td>6.1.1<\/td><td><\/td><td>orca<\/td><td>2025\/12\/05<\/td><td>openmpi418, avx2<\/td><\/tr><tr><td><\/td><td>6.1.0<\/td><td>&nbsp;<\/td><td>orca<\/td><td>2025\/07\/16<\/td><td>openmpi418<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<figure class=\"wp-block-table is-style-stripes\"><table class=\"has-fixed-layout\"><thead><tr><th>\u30d7\u30ed\u30b0\u30e9\u30e0\u540d<\/th><th><div class=\"block-editor-rich-text__editable rich-text\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" aria-label=\"\u672c\u6587\u30bb\u30eb\u306e\u30c6\u30ad\u30b9\u30c8\">\u30d0\u30fc\u30b8\u30e7\u30f3<\/div><\/th><th><div class=\"block-editor-rich-text__editable rich-text\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" aria-label=\"\u672c\u6587\u30bb\u30eb\u306e\u30c6\u30ad\u30b9\u30c8\">\u30ea\u30d3\u30b8\u30e7\u30f3<\/div><\/th><th><div class=\"block-editor-rich-text__editable rich-text\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" aria-label=\"\u672c\u6587\u30bb\u30eb\u306e\u30c6\u30ad\u30b9\u30c8\">\u30b3\u30de\u30f3\u30c9<\/div><\/th><th><div class=\"block-editor-rich-text__editable rich-text\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" aria-label=\"\u672c\u6587\u30bb\u30eb\u306e\u30c6\u30ad\u30b9\u30c8\">\u5c0e\u5165\/\u66f4\u65b0\u65e5<\/div><\/th><th><div class=\"block-editor-rich-text__editable rich-text\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" aria-label=\"\u672c\u6587\u30bb\u30eb\u306e\u30c6\u30ad\u30b9\u30c8\">\u5099\u8003<\/div><\/th><\/tr><\/thead><tbody><tr><td><div class=\"block-editor-rich-text__editable rich-text\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" aria-label=\"\u672c\u6587\u30bb\u30eb\u306e\u30c6\u30ad\u30b9\u30c8\">Slurm<\/div><\/td><td><div class=\"block-editor-rich-text__editable rich-text\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" aria-label=\"\u672c\u6587\u30bb\u30eb\u306e\u30c6\u30ad\u30b9\u30c8\">20.11.9<\/div><\/td><td><br><div class=\"block-editor-rich-text__editable rich-text\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" aria-label=\"\u672c\u6587\u30bb\u30eb\u306e\u30c6\u30ad\u30b9\u30c8\"><\/div><\/td><td><div class=\"block-editor-rich-text__editable rich-text\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" aria-label=\"\u672c\u6587\u30bb\u30eb\u306e\u30c6\u30ad\u30b9\u30c8\">sbatch, squeue, scancel<\/div><\/td><td><div class=\"block-editor-rich-text__editable rich-text\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" aria-label=\"\u672c\u6587\u30bb\u30eb\u306e\u30c6\u30ad\u30b9\u30c8\">2025\/08\/20<\/div><\/td><td>from DNF<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">\u30b3\u30f3\u30d1\u30a4\u30e9\u30fb\u30e9\u30a4\u30d6\u30e9\u30ea<\/h2>\n\n\n\n<figure class=\"wp-block-table is-style-stripes\"><table><thead><tr><th>\u540d\u524d<\/th><th>\u30d0\u30fc\u30b8\u30e7\u30f3<\/th><th>\u5099\u8003<\/th><\/tr><\/thead><tbody><tr><td>GCC<\/td><td>8.30*<\/td><td>&nbsp;<\/td><\/tr><tr><td>&nbsp;<\/td><td>11.2.1<\/td><td>scl enable gcc-toolset-11 bash<\/td><\/tr><tr><td><\/td><td>13.0<\/td><td>scl enable gcc-toolset-13 bash<\/td><\/tr><tr><td>CUDA<\/td><td>13.0*<\/td><td>Driver Version: 580.65.06<\/td><\/tr><tr><td><\/td><td>12.9<\/td><td>(for GROMACS 2025.2)<\/td><\/tr><tr><td><\/td><td>12.8<\/td><td>(for AmberTools 25)<\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>\u5185\u90e8\u5c02\u7528\u30da\u30fc\u30b8: \u8a08\u7b97\u6a5f\u5229\u7528\u306e\u624b\u5f15\u304d \u30d1\u30c3\u30b1\u30fc\u30b8\u30d7\u30ed\u30b0\u30e9\u30e0\u4e00 &#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"om_disable_all_campaigns":false,"_uag_custom_page_level_css":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"_locale":"ja","_original_post":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/?page_id=346","footnotes":""},"class_list":["post-346","page","type-page","status-publish","hentry","ja"],"aioseo_notices":[],"uagb_featured_image_src":{"full":false,"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false,"onepress-blog-small":false,"onepress-small":false,"onepress-medium":false},"uagb_author_info":{"display_name":"RCY","author_link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/author\/charlesy\/"},"uagb_comment_info":0,"uagb_excerpt":"\u5185\u90e8\u5c02\u7528\u30da\u30fc\u30b8: \u8a08\u7b97\u6a5f\u5229\u7528\u306e\u624b\u5f15\u304d \u30d1\u30c3\u30b1\u30fc\u30b8\u30d7\u30ed\u30b0\u30e9\u30e0\u4e00 ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/346","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/comments?post=346"}],"version-history":[{"count":119,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/346\/revisions"}],"predecessor-version":[{"id":6925,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/346\/revisions\/6925"}],"wp:attachment":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media?parent=346"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}