{"id":63,"date":"2012-05-30T19:44:39","date_gmt":"2012-05-31T01:44:39","guid":{"rendered":""},"modified":"2012-09-12T16:28:37","modified_gmt":"2012-09-12T07:28:37","slug":"\u5c0f\u898f\u6a21\u30bf\u30f3\u30d1\u30af\u8ceatrpcage\u306e\u7d50\u6676\u69cb\u9020\u306e\u7cbe\u7dfb\u5316","status":"publish","type":"post","link":"https:\/\/www.cenav.org\/kdb\/?p=63","title":{"rendered":"\u5c0f\u898f\u6a21\u30bf\u30f3\u30d1\u30af\u8ceaTrpCage\u306e\u7d50\u6676\u69cb\u9020\u306e\u7cbe\u7dfb\u5316"},"content":{"rendered":"<h3 id=\"kdb_body\">\u6982\u8981<\/h3>\n<p>FMO\u6cd5\u306b\u57fa\u3065\u304f\u90e8\u5206\u69cb\u9020\u6700\u9069\u5316\u306b\u3088\u308a\u3001\u5b9f\u9a13\u69cb\u9020\u306e\u7cbe\u5bc6\u5316\u3092\u884c\u3063\u305f\u3002\u30a2\u30df\u30ce\u9178-\u30a2\u30df\u30ce\u9178\u9593\u3084\u30a2\u30df\u30ce\u9178-\u30ea\u30ac\u30f3\u30c9\u9593\u306a\u3069\u306e\u76f8\u4e92\u4f5c\u7528\u3092\u89e3\u6790\u3059\u308b\u4e0a\u3067\u3088\u308a \u4fe1\u983c\u3067\u304d\u308b\u7acb\u4f53\u69cb\u9020\u3092\u5f97\u308b\u3053\u3068\u306f\u6975\u3081\u3066\u91cd\u8981\u3067\u3042\u308b\u304c\u3001ABINIT-MP\u3067\u306fMP2\u30ec\u30d9\u30eb\u306e\u90e8\u5206\u69cb\u9020\u6700\u9069\u5316\u306b\u3088\u308a\u3001&pi;\/&pi;\u3084CH\/&pi;\u76f8\u4e92\u4f5c\u7528\u306a\u3069\u96fb\u5b50\u76f8\u95a2 \u306e\u8003\u616e\u304c\u5fc5\u8981\u306a\u76f8\u4e92\u4f5c\u7528\u3092\u6301\u3064\u30bf\u30f3\u30d1\u30af\u8cea\u3082\u69cb\u9020\u6700\u9069\u5316\u3067\u304d\u308b\u3002\u307e\u305f\u3001FMO\u6cd5\u306b\u57fa\u3065\u304f\u90e8\u5206\u69cb\u9020\u6700\u9069\u5316\u3067\u306f\u3001\u6700\u9069\u5316\u9818\u57df\u3068\u5468\u8fba\u306e\u30a8\u30cd\u30eb\u30ae\u30fc\u52fe\u914d\u306e\u307f\u3092\u9078\u629e\u7684 \u306b\u8a08\u7b97\u3059\u308b\u3053\u3068\u306b\u3088\u308a\u3001\u8a08\u7b97\u30b3\u30b9\u30c8\u306e\u9762\u3067\u52b9\u7387\u7684\u306a\u69cb\u9020\u6700\u9069\u5316\u3092\u884c\u3046\u3053\u3068\u304c\u3067\u304d\u308b\u3002\u3053\u308c\u306f\u3001\u5927\u898f\u6a21\u30bf\u30f3\u30d1\u30af\u8cea\u306b\u304a\u3044\u3066\u30d5\u30a1\u30fc\u30de\u30b3\u30db\u30a2\u306e\u307f\u3092\u6700\u9069\u5316\u3059\u308b\u5834\u5408\u306b \u304a\u3044\u3066\u7279\u306b\u6709\u7528\u3067\u3042\u308b\u3068\u8003\u3048\u3089\u308c\u308b\u3002\u30d5\u30e9\u30b0\u30e1\u30f3\u30c8\u5206\u5b50\u8ecc\u9053\u6cd5\u3092\u7528\u3044\u3066\u30bf\u30f3\u30d1\u30af\u8cea\uff0d\u30ea\u30ac\u30f3\u30c9\u8907\u5408\u4f53\u306e\u96fb\u5b50\u72b6\u614b\u8a08\u7b97\u3092\u884c\u3046\u3068\u3068\u3082\u306b\u3001\u30d5\u30e9\u30b0\u30e1\u30f3\u30c8\u9593\u76f8\u4e92\u4f5c\u7528\u30a8 \u30cd\u30eb\u30ae\u30fc\u89e3\u6790\u306b\u3088\u308a\u3001\u30ea\u30ac\u30f3\u30c9\u3068\u5404\u30a2\u30df\u30ce\u9178\u6b8b\u57fa\u3068\u306e\u76f8\u4e92\u4f5c\u7528\u3092\u5b9a\u91cf\u7684\u306b\u8a55\u4fa1\u3059\u308b\u3002<\/p>\n<p><img alt=\"\" src=\"\/kdb\/out\/i63_1.png\" \/><\/p>\n<h3 id=\"kdb_field_related_modules\">\u95a2\u9023\u30e2\u30b8\u30e5\u30fc\u30eb<\/h3>\n<p>BioStation Viewer (Ver. 13.01)<\/p>\n<h3 id=\"kdb_field_sim_model\">\u89e3\u6790\u30e2\u30c7\u30eb<\/h3>\n<p>\u5c0f\u898f\u6a21\u30bf\u30f3\u30d1\u30af\u8cea TrpCage<br \/>\n\tPDB ID: 1L2Y<br \/>\n\t\u539f\u5b50\u6570304\u3001\u6b8b\u57fa\u657020\u3001\u30d5\u30e9\u30b0\u30e1\u30f3\u30c8\u657020<\/p>\n<h3 id=\"kdb_field_calc_condition\">\u8a08\u7b97\u6761\u4ef6<\/h3>\n<p>\u30fbFMO2-MP2\/6-31G<\/p>\n<p>\u30fbMP2\u6cd5\u306b\u57fa\u3065\u304f\u30a8\u30cd\u30eb\u30ae\u30fc\u52fe\u914d\u8a08\u7b97<\/p>\n<p>\u30fbBFGS\u6cd5\u306b\u57fa\u3065\u304f\u69cb\u9020\u6700\u9069\u5316\u8a08\u7b97<\/p>\n<p>\u30fb\u90e8\u5206\u30a8\u30cd\u30eb\u30ae\u30fc\u52fe\u914d\u8a08\u7b97<\/p>\n<p>\u30fb\u771f\u7a7a\u4e2d \u30fb\u30d5\u30e9\u30b0\u30e1\u30f3\u30c8\u5206\u5272\uff1a\u4e3b\u9396\u5358\u4f4d<\/p>\n<h3 id=\"kdb_field_exe_env\">\u5b9f\u884c\u74b0\u5883<\/h3>\n<p>MPI<\/p>\n<p>CPU: Xeon 3.4 GHz 4\u30b3\u30a2 &times; 5\u30ce\u30fc\u30c9<\/p>\n<p>GPU: 6 GB\u30e1\u30e2\u30ea\/1 \u30d7\u30ed\u30bb\u30b9<\/p>\n<p>Memory:<\/p>\n<p>HDD:<\/p>\n<h3 id=\"kdb_field_description_simu_case\">\u8a73\u7d30\u8aac\u660e<\/h3>\n<ul>\n<li>\n\t\t\u89e3\u6790\u6642\u9593\uff1a<\/li>\n<\/ul>\n<p>\u90e8\u5206\u30a8\u30cd\u30eb\u30ae\u30fc\u52fe\u914d\u8a08\u7b971\u56de\u3042\u305f\u308a3.4\u6642\u9593 &times; \u69cb\u9020\u6700\u9069\u5316\u306b\u5fc5\u8981\u306a\u56de\u6570<br \/>\n\t\u6570\u65e5\u304b\u3089\u6570\u9031\u9593\u7a0b\u5ea6<\/p>\n<p>TrpCage\u5168\u4f53\u306e\u30a8\u30cd\u30eb\u30ae\u30fc\u52fe\u914d\u3092\u8a08\u7b97\u3057\u305f\u5834\u5408\uff08Full energy gradient\uff09\u3068\u6700\u9069\u5316\u9818\u57df\u3068\u305d\u306e\u5468\u8fba\u306e\u307f\u306e\u30a8\u30cd\u30eb\u30ae\u30fc\u52fe\u914d\u3092\u8a08\u7b97\u3057\u305f\u5834\u5408\uff08Partial energy gradient\uff09\u306e\u6700\u9069\u5316\u9818\u57df\u306e\u30a8\u30cd\u30eb\u30ae\u30fc\u52fe\u914d\u306e\u5024\uff08X,Y,Z\u6210\u5206\uff09\u3092\u30d7\u30ed\u30c3\u30c8\u3057\u305f\u3002\u76f8\u95a2\u4fc2\u6570\u306f0.97\u3068\u306a\u308a\u3001\u5341\u5206\u306a\u7cbe\u5ea6\u304c\u4fdd\u6301\u3055\u308c\u3066\u3044\u308b\u3002<\/p>\n<p><img alt=\"\" src=\"\/kdb\/out\/i63_2.png\" \/><\/p>\n<p>FMO-HF\u6cd5\u3068FMO-MP2\u6cd5\u306b\u3088\u308b\u6700\u9069\u5316\u69cb\u9020(\u8d64)\u3068\u5b9f\u9a13\u69cb\u9020(\u7dd1)\u3092\u91cd\u306d\u5408\u308f\u305b\u305f\u3082\u306e\u3092\u793a\u3059\u3002FMO-HF\u6cd5\u306e\u7d50\u679c\u3067\u306f\u3001TYR3\u306e\u30d5\u30a7\u30ce\u30fc\u30eb\u74b0 \u304c\u5b9f\u9a13\u69cb\u9020\u304b\u3089\u5927\u304d\u304f\u305a\u308c\u3066\u3044\u308b\u3053\u3068\u304c\u308f\u304b\u308b\u3002\u3053\u308c\u306fHF\u30ec\u30d9\u30eb\u3067\u306fTYR3\u3068TRP6\u306e&pi;\/&pi;\u76f8\u4e92\u4f5c\u7528\u304c\u8a18\u8ff0\u3067\u304d\u306a\u3044\u305f\u3081\u3067\u3042\u308b\u3068\u8003\u3048\u3089\u308c\u308b\u3002\u4e00\u65b9\u3001 FMO-MP2\u306e\u7d50\u679c\u3067\u306f\u5927\u304d\u306a\u69cb\u9020\u5909\u5316\u306f\u898b\u3089\u308c\u306a\u3044\u3002\u3053\u308c\u306fMP2\u6cd5\u306b\u3088\u3063\u3066\u96fb\u5b50\u76f8\u95a2\u304c\u8003\u616e\u3055\u308c\u3001&pi;\/&pi;\u3084CH\/&pi;\u306a\u3069\u306e\u76f8\u4e92\u4f5c\u7528\u304c\u8a18\u8ff0\u3055\u308c\u3066\u3044\u308b\u305f\u3081 \u3068\u8003\u3048\u3089\u308c\u308b\u3002<\/p>\n<p><img alt=\"\" src=\"\/kdb\/out\/i63_3.png\" \/><\/p>\n<h3 id=\"kdb_field_reference_info\">\u53c2\u8003\u6587\u732e<\/h3>\n<p>Y. Mochizuki, T. Nakano, Y. Komeiji, K. Yamashita, Y. Okiyama, H. Yoshikawa and H. Yamataka, Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient, Chem. Phys. Lett., Vol. 504, pp.95-99, (2011).<br \/>\n\tT. Tsukamoto, Y. Mochizuki, N. Watanabe, K. Fukuzawa and T. Nakano, Partial geometry optimization with FMO-MP2 gradient: application to TrpCage, submitted.<\/p>\n<h3 id=\"kdb_field_charac_keyword\">\u7279\u5fb4\u691c\u7d22\u30ad\u30fc\u30ef\u30fc\u30c9<\/h3>\n<p>\u30d5\u30e9\u30b0\u30e1\u30f3\u30c8\u5206\u5b50\u8ecc\u9053\u6cd5<br \/>\nMP2\u6cd5<br \/>\n\u69cb\u9020\u6700\u9069\u5316<br \/>\n\u90e8\u5206\u30a8\u30cd\u30eb\u30ae\u30fc\u52fe\u914d<br \/>\n\u30bf\u30f3\u30d1\u30af\u8cea<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u6982\u8981 FMO\u6cd5\u306b\u57fa\u3065\u304f\u90e8\u5206\u69cb\u9020\u6700\u9069\u5316\u306b\u3088\u308a\u3001\u5b9f\u9a13\u69cb\u9020\u306e\u7cbe\u5bc6\u5316\u3092\u884c\u3063\u305f\u3002\u30a2\u30df\u30ce\u9178-\u30a2\u30df\u30ce\u9178\u9593\u3084\u30a2\u30df\u30ce\u9178-\u30ea\u30ac\u30f3\u30c9\u9593\u306a\u3069\u306e\u76f8\u4e92\u4f5c\u7528\u3092\u89e3\u6790\u3059\u308b\u4e0a\u3067\u3088\u308a \u4fe1\u983c\u3067\u304d\u308b\u7acb\u4f53\u69cb\u9020\u3092\u5f97\u308b\u3053\u3068\u306f\u6975\u3081\u3066\u91cd\u8981\u3067\u3042\u308b\u304c\u3001ABINIT-MP\u3067\u306fM [<a title=\"\u4f1a\u54e1\u767b\u9332\u304c\u5fc5\u8981\u3067\u3059\" href=\"https:\/\/www.cenav.org\/kdb\/?p=63\">\u5168\u6587\u3092\u8aad\u3080<\/a>]<\/p>\n","protected":false},"author":54,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[104,54],"tags":[],"_links":{"self":[{"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/posts\/63"}],"collection":[{"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/users\/54"}],"replies":[{"embeddable":true,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=63"}],"version-history":[{"count":0,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/posts\/63\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=63"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=63"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=63"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}