{"id":2415,"date":"2018-12-28T18:47:43","date_gmt":"2018-12-28T09:47:43","guid":{"rendered":"https:\/\/www.hpc.co.jp\/chem\/?page_id=2415"},"modified":"2020-02-19T12:48:28","modified_gmt":"2020-02-19T03:48:28","slug":"c_md_basic","status":"publish","type":"page","link":"https:\/\/www.hpc.co.jp\/chem\/library\/c_md_basic\/","title":{"rendered":"\u5206\u5b50\u52d5\u529b\u5b66\u306e\u57fa\u790e\u77e5\u8b58"},"content":{"rendered":"<div id=\"page_head\">\n<div class=\"inviewfadeIn animated fadeIn\">\n<div class=\"top_title_science clearfix\">\n<div class=\"left\"> <span class=\"en\">Science as a Service<br \/>\n        Software<\/span><\/p>\n<h1 class=\"jp\">\u8a08\u7b97\u5316\u5b66<\/h1>\n<\/p><\/div>\n<div class=\"right\">\u6280\u8853\u60c5\u5831<\/div>\n<\/p><\/div>\n<\/p><\/div>\n<\/div>\n<div id=\"page_container\">\n<div class=\"pnkz\"><a href=\"\/\">\u30db\u30fc\u30e0<\/a> &gt; <a href=\"\/hpc\/\">HPC\u30fbDL\u30fbAI<\/a> &gt; <a href=\"\/chem\/\">\u8a08\u7b97\u5316\u5b66<\/a> &gt; <a href=\"\/chem\/library\/\">\u6280\u8853\u60c5\u5831<\/a> &gt; \u5206\u5b50\u52d5\u529b\u5b66\u306e\u57fa\u790e\u77e5\u8b58<\/div>\n<section class=\"container\">\n<div class=\"block\">\n<h2 class=\"title_full\">\u5206\u5b50\u52d5\u529b\u5b66\u306e\u57fa\u790e\u77e5\u8b58<\/h2>\n<div class=\"innerWrap\">\n<h3 class=\"title_gr\">1. \u5206\u5b50\u52d5\u529b\u5b66\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u30e2\u30c7\u30eb<\/h3>\n<div class=\"text_area_90\">\n<div class=\"col2_area\">\n<div class=\"left\">\n<p class=\"mar10b\">\u5206\u5b50\u52d5\u529b\u5b66\u3067\u306f\u57fa\u672c\u7684\u306b\u539f\u5b50\u306e\u904b\u52d5\u3060\u3051\u3092\u6271\u3046\u3002\u96fb\u5b50\u3084\u539f\u5b50\u6838\u306b\u3064\u3044\u3066\u306f\u8003\u3048\u305a\u3001\u4ee3\u308f\u308a\u306b\u30e2\u30c7\u30eb\u5316\u3055\u308c\u305f\u529b\u5834\u30dd\u30c6\u30f3\u30b7\u30e3\u30eb\u95a2\u6570\u3092\u4f7f\u3063\u3066\u3001\u539f\u5b50\u540c\u58eb\u306b\u50cd\u304f\u76f8\u4e92\u4f5c\u7528\u3092\u8868\u73fe\u3057\u3066\u3044\u308b\u3002\u4e00\u90e8\u306e\u73fe\u8c61\u3092\u9664\u3051\u3070\u307b\u3068\u3093\u3069\u306e\u5834\u5408\u3001\u539f\u5b50\u306e\u904b\u52d5\u306f\u53e4\u5178\u7684\u306b\u6271\u3046\u3053\u3068\u304c\u3067\u304d\u308b\u3068\u8003\u3048\u3001Newton\u65b9\u7a0b\u5f0f\u3092\u5206\u5b50\u52d5\u529b\u5b66\u306e\u57fa\u790e\u65b9\u7a0b\u5f0f\u3068\u3057\u3066\u3044\u308b\u3002<\/p>\n<div class=\"img_border_gr mar40b\">\n<div class=\"img_area\">\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.hpc.co.jp\/chem\/wp-content\/uploads\/sites\/4\/chem\/library\/eq_newton.png\" alt=\"\" width=\"186\" height=\"84\" class=\"alignnone size-full wp-image-2412\" \/>\n<\/div>\n<\/div>\n<\/div>\n<p><!-- left --><\/p>\n<div class=\"right\">\n<div class=\"img_border_gr\">\n<div class=\"img_area\">\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.hpc.co.jp\/chem\/wp-content\/uploads\/sites\/4\/chem\/library\/md_snapshot_small.jpg\" alt=\"\" width=\"200\" height=\"200\" class=\"alignnone size-full wp-image-2413\" \/>\n<\/div>\n<\/div>\n<\/div>\n<p><!-- right -->\n<\/div>\n<p class=\"mar20b\">\u5206\u5b50\u52d5\u529b\u5b66\u3067\u306f\u6709\u9650\u6e29\u5ea6\u74b0\u5883\u3067\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u304c\u53ef\u80fd\u3067\u3042\u308a\u3001\u30a2\u30d7\u30ea\u30b1\u30fc\u30b7\u30e7\u30f3\u306b\u3088\u3063\u3066\u306f\u9ad8\u6e29\u90e8\u3068\u4f4e\u6e29\u90e8\u3092\u8a2d\u5b9a\u3057\u305f\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3084\u3001\u5916\u7684\u306b\u96fb\u5834\u3084\u529b\u3092\u4e0e\u3048\u308b\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3082\u53ef\u80fd\u3067\u3042\u308b\u3002<\/p>\n<div class=\"col2_area\">\n<div class=\"left\">\n<p class=\"mar20b\">\u8a08\u7b97\u7cbe\u5ea6\u306f\u30dd\u30c6\u30f3\u30b7\u30e3\u30eb\u95a2\u6570\u306e\u51fa\u6765\u306b\u5de6\u53f3\u3055\u308c\u308b\u3002\u30dd\u30c6\u30f3\u30b7\u30e3\u30eb\u95a2\u6570\u306f\u591a\u6570\u306e\u529b\u5834\u30d1\u30e9\u30e1\u30fc\u30bf\u3067\u69cb\u6210\u3055\u308c\u3066\u304a\u308a\u3001\u3053\u308c\u3089\u306e\u30d1\u30e9\u30e1\u30fc\u30bf\u306f\u91cf\u5b50\u5316\u5b66\u8a08\u7b97\u3084\u5b9f\u9a13\u5024\u3092\u4f7f\u3063\u3066\u30c8\u30ec\u30fc\u30cb\u30f3\u30b0\u3055\u308c\u3066\u3044\u308b\u3002\u30dd\u30c6\u30f3\u30b7\u30e3\u30eb\u95a2\u6570\u306e\u95a2\u6570\u5f62\u3084\u529b\u5834\u30d1\u30e9\u30e1\u30fc\u30bf\u30bb\u30c3\u30c8\u306f\u76ee\u7684\u3068\u3059\u308b\u5206\u5b50\u7cfb\u306b\u5408\u308f\u305b\u3066\u7528\u610f\u3055\u308c\u3066\u3044\u308b\u3002\u4f8b\u3048\u3070\u540c\u3058\u70ad\u7d20\u539f\u5b50\u3067\u3082\u6709\u6a5f\u5206\u5b50\u3068\u30b0\u30e9\u30d5\u30a1\u30a4\u30c8\u3067\u306f\u6027\u8cea\u304c\u7570\u306a\u308b\u305f\u3081\u3001\u7570\u306a\u308b\u529b\u5834\u30d1\u30e9\u30e1\u30fc\u30bf\u3092\u3042\u3066\u304c\u3046\u3053\u3068\u304c\u591a\u3044\u3002<\/p>\n<p class=\"mar0b\">\u8fd1\u5e74\u3067\u306f\u30dd\u30c6\u30f3\u30b7\u30e3\u30eb\u306e\u8a08\u7b97\u306b\u30e2\u30c7\u30eb\u30dd\u30c6\u30f3\u30b7\u30e3\u30eb\u3092\u4f7f\u3046\u306e\u3067\u306f\u306a\u304f\u3001\u91cf\u5b50\u5316\u5b66\u8a08\u7b97\u3092\u5229\u7528\u3059\u308b\u3053\u3068\u3067\u5fdc\u7528\u7bc4\u56f2\u3092\u5e83\u3052\u305f\u65b9\u6cd5\u3082\u767b\u5834\u3057\u3066\u3044\u308b\u3002<\/p>\n<\/div>\n<div class=\"right\">\n<div class=\"img_border_gr\">\n<div class=\"img_area\">\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.hpc.co.jp\/chem\/wp-content\/uploads\/sites\/4\/chem\/library\/potential_harmonic.png\" alt=\"\" width=\"213\" height=\"236\" class=\"alignnone size-full wp-image-2411\" \/>\n<\/div>\n<\/div>\n<\/div>\n<p><!-- right -->\n<\/div>\n<p><!-- col2_area --><\/p>\n<div class=\"img_border_gr mar40b\">\n<div class=\"img_area\">\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.hpc.co.jp\/chem\/wp-content\/uploads\/sites\/4\/chem\/library\/table_forcefield1.png\" alt=\"\" width=\"787\" height=\"317\" class=\"alignnone size-full wp-image-2407\" \/>\n<\/div>\n<div class=\"img_area\">\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.hpc.co.jp\/chem\/wp-content\/uploads\/sites\/4\/chem\/library\/table_forcefield2.png\" alt=\"\" width=\"956\" height=\"232\" class=\"alignnone size-full wp-image-2410\" \/>\n<\/div>\n<\/div>\n<\/div>\n<h3 class=\"title_gr\">2. \u53e4\u5178\u5206\u5b50\u52d5\u529b\u5b66<\/h3>\n<div class=\"text_area_90\">\n<p class=\"mar20b\">\u5206\u5b50\u52d5\u529b\u5b66\u3068\u3044\u3063\u305f\u5834\u5408\u3001\u901a\u5e38\u53e4\u5178\u5206\u5b50\u52d5\u529b\u5b66\u306e\u3053\u3068\u3092\u6307\u3059\u3002\u30e2\u30c7\u30eb\u30dd\u30c6\u30f3\u30b7\u30e3\u30eb\u95a2\u6570\u3092\u4f7f\u3063\u3066\u3001\u539f\u5b50\u9593\u306e\u76f8\u4e92\u4f5c\u7528\u3092\u8a18\u8ff0\u3057\u3066\u3044\u308b\u3002<\/p>\n<p class=\"mar20b\">\n\u30dd\u30c6\u30f3\u30b7\u30e3\u30eb\u306f\u5bfe\u8c61\u3054\u3068\u306b\u30c1\u30e5\u30fc\u30cb\u30f3\u30b0\u3055\u308c\u3066\u304a\u308a\u3001\u4f8b\u3048\u3070\u6709\u6a5f\u5206\u5b50\u3067\u3042\u308c\u3070AMBER\u529b\u5834\u3001\u91d1\u5c5e\u3067\u3042\u308c\u3070EAM\u529b\u5834\u3044\u3063\u305f\u5177\u5408\u306b\u7570\u306a\u308b\u529b\u5834\u304c\u7528\u610f\u3055\u308c\u3066\u3044\u308b\u3002<\/p>\n<p class=\"mar20b\">\n\u4f4e\u30b9\u30da\u30c3\u30af\u306e\u8a08\u7b97\u6a5f\u3067\u3082\u6570\u4e07\u539f\u5b50\u3001\u6570\u30ca\u30ce\u79d2\u7a0b\u5ea6\u306e\u8a08\u7b97\u304c\u53ef\u80fd\u3067\u3042\u308b\u3002<\/p>\n<div class=\"img_border_gr mar40b\">\n<div class=\"img_area\">\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.hpc.co.jp\/chem\/wp-content\/uploads\/sites\/4\/chem\/library\/potential_amber_small.png\" alt=\"\" width=\"600\" height=\"122\" class=\"alignnone size-full wp-image-2409\" \/>\n<\/div>\n<div class=\"caption\" style=\"text-align:center;\">AMBER\u529b\u5834\u306e\u30dd\u30c6\u30f3\u30b7\u30e3\u30eb\u95a2\u6570<br \/>\n(\u8d64\u5b57\u306f\u529b\u5834\u30d1\u30e9\u30e1\u30fc\u30bf\u3001\u7dd1\u5b57\u306f\u539f\u5b50\u96fb\u8377)<\/div>\n<\/div>\n<p class=\"mar20b\">\u4e3b\u306a\u5bfe\u5fdc\u30a2\u30d7\u30ea\u30b1\u30fc\u30b7\u30e7\u30f3<\/p>\n<ul class=\"li_square\">\n<li><a href=\"\/chem\/software\/amber\/\">AMBER<\/a>\n<\/li>\n<li><a href=\"\/chem\/software\/gromacs\/\">GROMACS<\/a>\n<\/li>\n<li><a href=\"\/chem\/software\/lammps\/\">LAMMPS<\/a>\n<\/li>\n<\/ul>\n<\/div>\n<h3 class=\"title_gr\">3. QM\/MM\u5206\u5b50\u52d5\u529b\u5b66<\/h3>\n<div class=\"text_area_90\">\n<div class=\"col2_area\">\n<div class=\"left\">\n<p class=\"mar20b\">AMBER\u529b\u5834\u306a\u3069\u306e\u591a\u304f\u306e\u53e4\u5178\u529b\u5834\u3067\u306f\u5316\u5b66\u53cd\u5fdc\u3092\u6271\u3046\u3053\u3068\u304c\u3067\u304d\u306a\u3044\u3002\u307e\u305f\u3001\u7cbe\u5ea6\u306e\u89b3\u70b9\u3067\u53e4\u5178\u529b\u5834\u3067\u306f\u3046\u307e\u304f\u5bfe\u5fdc\u3067\u304d\u306a\u3044\u3053\u3068\u3082\u3042\u308b\u3002\u305d\u306e\u3088\u3046\u306a\u5834\u5408\u306b\u306f\u91cf\u5b50\u5316\u5b66\u3092\u983c\u3089\u3056\u308b\u3092\u5f97\u306a\u3044\u3002<\/p>\n<p class=\"mar20b\">\n\u3057\u304b\u3057\u3001\u91cf\u5b50\u5316\u5b66\u8a08\u7b97\u306f\u9ad8\u7cbe\u5ea6\u3067\u3042\u308b\u3082\u306e\u306e\u3001\u8a08\u7b97\u30b3\u30b9\u30c8\u304c\u975e\u5e38\u306b\u9ad8\u3044\u305f\u3081\u3001\u3059\u3079\u3066\u3092\u91cf\u5b50\u5316\u5b66\u3067\u884c\u3046\u306b\u306f\u9650\u5ea6\u304c\u3042\u308b\u3002\u305d\u306e\u3088\u3046\u306a\u5834\u5408\u306b\u306f\u5fc5\u8981\u306a\u90e8\u4f4d\u306b\u306e\u307f\u306b\u91cf\u5b50\u5316\u5b66\u8a08\u7b97\u3092\u9069\u7528\u3059\u308bQM\/MM\u5206\u5b50\u52d5\u529b\u5b66\u6cd5\u3092\u4f7f\u3046\u3053\u3068\u304c\u3042\u308b\u3002<\/p>\n<p class=\"mar20b\">\n\u91cf\u5b50\u5316\u5b66\u3092\u4f7f\u3046\u90e8\u5206\u306b\u306f\u3001\u534a\u7d4c\u9a13\u7684\u624b\u6cd5\u3084ab initio\u6cd5\u3092\u9069\u7528\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u308b\u3002\u91cf\u5b50\u5316\u5b66\u8a08\u7b97\u3092\u884c\u3063\u3066\u3044\u308b\u305f\u3081\u3001\u96fb\u5b50\u72b6\u614b\u304c\u304b\u304b\u308f\u308b\u30d7\u30ed\u30d1\u30c6\u30a3\uff08HOMO\/LUMO\u3001\u5206\u5149\u30b9\u30da\u30af\u30c8\u30eb\u306a\u3069\uff09\u304c\u5f97\u3089\u308c\u308b\u306e\u3082\u7279\u5fb4\u3067\u3042\u308b\u3002<\/p>\n<p class=\"mar20b\">\n\u8a08\u7b97\u5bfe\u8c61\u3084\u91cf\u5b50\u5316\u5b66\u306e\u624b\u6cd5\u306b\u3082\u3088\u308b\u304c\u3001\u91cf\u5b50\u5316\u5b66\u3067\u6271\u3046\u90e8\u4f4d\u304c\uff5e100\u539f\u5b50\u306e\u7cfb\u3067\u6570\u767eps\u7a0b\u5ea6\u306e\u8a08\u7b97\u304c\u53ef\u80fd\u3067\u3042\u308b\u3002<\/p>\n<p class=\"mar20b\">\u4e3b\u306a\u5bfe\u5fdc\u30a2\u30d7\u30ea\u30b1\u30fc\u30b7\u30e7\u30f3<\/p>\n<ul class=\"li_square\">\n<li><a href=\"\/chem\/software\/amber\/\">AMBER<\/a>\n<\/li>\n<\/ul>\n<\/div>\n<p><!--left --><\/p>\n<div class=\"right\">\n<div class=\"img_border_gr mar40b\">\n<div class=\"img_area\">\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.hpc.co.jp\/chem\/wp-content\/uploads\/sites\/4\/chem\/library\/qmmm_model_small.png\" alt=\"\" width=\"200\" height=\"140\" class=\"alignnone size-full wp-image-2408\" \/>\n<\/div>\n<div class=\"img_area\">\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.hpc.co.jp\/chem\/wp-content\/uploads\/sites\/4\/chem\/library\/qmmm_image_small.jpg\" alt=\"\" width=\"200\" height=\"170\" class=\"alignnone size-full wp-image-2406\" \/>\n<\/div>\n<\/div>\n<\/div>\n<p><!--right -->\n<\/div>\n<p><!--col2_area --><\/p>\n<\/div>\n<h3 class=\"title_gr\">4. \u91cf\u5b50\u5206\u5b50\u52d5\u529b\u5b66<\/h3>\n<div class=\"text_area_90\">\n<p class=\"mar20b\">\u7cfb\u306e\u3059\u3079\u3066\u3092\u91cf\u5b50\u5316\u5b66\u7684\u306b\u884c\u3046\u624b\u6cd5\u306f\u91cf\u5b50\u5206\u5b50\u52d5\u529b\u5b66\u3068\u547c\u3070\u308c\u3001Car-Parrinello\u6cd5\u306f\u305d\u306e\u65b9\u6cd5\u306e\u4e00\u3064\u3067\u3042\u308b\u3002Car-Parrinello\u6cd5\u3067\u306f\u3001\u96fb\u5b50\u306e\u6ce2\u52d5\u95a2\u6570\u306b\u4eee\u60f3\u306e\u8cea\u91cf\u3092\u5b9a\u7fa9\u3057\u3001\u6838\u306e\u904b\u52d5\u65b9\u7a0b\u5f0f\u3068\u6ce2\u52d5\u95a2\u6570\u306e\u904b\u52d5\u65b9\u7a0b\u5f0f\u3092\u4e26\u5217\u3057\u3066\u89e3\u304f\u624b\u6cd5\u3067\u3042\u308a\u3001\u6838\u306e\u904b\u52d5\u306b\u96fb\u5b50\u72b6\u614b\u304c\u8ffd\u5f93\u3059\u308b\u5f62\u3068\u306a\u3063\u3066\u3044\u308b\u3002\u3053\u306e\u5927\u80c6\u306a\u8fd1\u4f3c\u306e\u7d50\u679c\u3001\u5b9f\u7528\u7684\u306a\u8a08\u7b97\u901f\u5ea6\u306e\u5b9f\u73fe\u306b\u5927\u304d\u304f\u8fd1\u3065\u3044\u305f\u3002\u73fe\u5728\u3067\u306f\u3001\u65ad\u71b1\u8fd1\u4f3c\u3092\u7528\u3044\u305a\u306b\u96fb\u5b50\u72b6\u614b\u3092\u6271\u3046\u975e\u65ad\u71b1\u5206\u5b50\u52d5\u529b\u5b66\u306a\u3069\u3001\u3055\u307e\u3056\u307e\u306a\u65b9\u6cd5\u304c\u8a66\u307f\u3089\u308c\u3066\u3044\u308b\u3002<\/p>\n<p class=\"mar20b\">\n\u975e\u5e38\u306b\u8a08\u7b97\u30b3\u30b9\u30c8\u306f\u9ad8\u304f\u3001100\u539f\u5b50\u4ee5\u4e0a\u306e\u8a08\u7b97\u306b\u306f\u5927\u578b\u306e\u8a08\u7b97\u6a5f\u304c\u5fc5\u8981\u3067\u3042\u308b\u3002<\/p>\n<p class=\"mar20b\">\u4e3b\u306a\u5bfe\u5fdc\u30a2\u30d7\u30ea\u30b1\u30fc\u30b7\u30e7\u30f3<\/p>\n<ul class=\"li_square mar20b\">\n<li><a href=\"\/product\/software\/cpmd\/\">CPMD<\/a>\n<\/li>\n<\/ul>\n<p class=\"mar20b\">\u7814\u7a76\u4e8b\u4f8b<\/p>\n<ul class=\"li_square mar20b\">\n<li><a href=\"https:\/\/www.nims.go.jp\/news\/press\/2013\/08\/p201308010.html\" target=\"_blank\">\u4eac\u30b3\u30f3\u30d4\u30e5\u30fc\u30bf\u3092\u7528\u3044\u3066\u30ea\u30c1\u30a6\u30e0\u30a4\u30aa\u30f3\u96fb\u6c60\u96fb\u89e3\u6db2\u306e\u9084\u5143\u53cd\u5fdc\u6a5f\u69cb\u3092\u89e3\u660e <small>(NIMS\u30d7\u30ec\u30ea\u30ea\u30fc\u30b9 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