CREST\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h2>\n
\u30b3\u30f3\u30d1\u30a4\u30eb\u6e08\u307f\u306e\u30d0\u30a4\u30ca\u30ea<\/a>\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066 \/usr\/local\/bin \u306b\u30b3\u30d4\u30fc\u3057\u3066\u3001sudo chmod +x \/usr\/local\/bin\/crest\u3002<\/p>\n\n\n\n conda-forge\u304b\u3089\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u307e\u3057\u305f\u3002<\/p>\n\n\n 9\u54e1\u74b0\u30e9\u30af\u30bf\u30e0\u5316\u5408\u7269Indolactam-V\u306e\u914d\u5ea7\u63a2\u7d22\u3092\u884c\u3044\u307e\u3059\u3002<\/p>\n ILV.xyz<\/strong><\/p>\n -gfn2 \u306fGFN2-xTB\u6cd5\u3092\u6307\u5b9a\u3059\u308b\u30aa\u30d7\u30b7\u30e7\u30f3\u3001-gbsa h2o \u306f\u6c34\u6eb6\u5a92\u548c\u30e2\u30c7\u30eb\u3001-ewin\u306f\u30a8\u30cd\u30eb\u30ae\u30fc\u95be\u5024\u30926 kcal\/mol\u4ee5\u5185\u3068\u6307\u5b9a\u3059\u308b\u3001-T \u306f\u8a08\u7b97\u306b\u4f7f\u7528\u3059\u308bCPU\uff08\u30d7\u30ed\u30bb\u30b9\uff09\u306e\u6570\u3002<\/p>\n \u51fa\u529b\u3055\u308c\u3066\u3044\u308b crest_conformers.xyz \u3092UCSF ChimeraX<\/a>\u3067\u958b\u3044\u3066\u69cb\u9020\u3092\u78ba\u8a8d\u3057\u307e\u3057\u305f\u3002<\/p>\n 33\u7a2e\u985e\u306e\u30b3\u30f3\u30db\u30de\u30fc\u304c\u542b\u307e\u308c\u3066\u304a\u308a\u3001cis<\/em>-amide\u578b\u306etwist\u3001fold\u30b3\u30f3\u30db\u30de\u30fc\u3001trans<\/em>-amide\u578b\u306esofa\u30b3\u30f3\u30db\u30de\u30fc<\/a>\u304c\u78ba\u8a8d\u3067\u304d\u307e\u3057\u305f\u3002NMR\u3067\u306f\u89b3\u6e2c\u3055\u308c\u306a\u3044fold\u30b3\u30f3\u30db\u30de\u30fc\u304c\u51fa\u3066\u304d\u3066\u3044\u307e\u3057\u305f\u304c\u3001\u3088\u308a\u6b63\u78ba\u306a\u8a08\u7b97\u306fGaussian\u306a\u308aORCA\u306a\u308a\u3067\u884c\u3048\u3070\u3088\u3044\u306e\u3067\u3001\u914d\u5ea7\u63a2\u7d22\u3068\u3057\u3066\u306f\u8a08\u7b97\u6642\u9593\u3001\u7cbe\u5ea6\u3068\u3082\u306b\u5341\u5206\u3060\u3068\u8003\u3048\u3089\u308c\u307e\u3059\u3002RDKit\u3092\u4f7f\u3063\u305f\u914d\u5ea7\u63a2\u7d22<\/a>\u3067\u306ftrans<\/em>-amide\u578b\u304c\u51fa\u73fe\u3057\u306a\u304b\u3063\u305f\u306e\u3067\u3001MD\u3092\u57fa\u306b\u3057\u305f\u914d\u5ea7\u63a2\u7d22\u304c\u5c11\u304f\u3068\u3082\u3053\u306e\u624b\u306e\u5316\u5408\u7269\u306b\u306f\u9069\u3057\u3066\u3044\u308b\u3053\u3068\u304c\u78ba\u8a8d\u3067\u304d\u307e\u3057\u305f\u3002<\/p>\n \uff08\u4e86\uff09<\/p>\n\n\n","protected":false},"excerpt":{"rendered":" $ conda config –add channels …<\/p>\n","protected":false},"author":1,"featured_media":5101,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","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\/?p=5094","footnotes":""},"categories":[5],"tags":[],"class_list":["post-5094","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-5","ja"],"aioseo_notices":[],"uagb_featured_image_src":{"full":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-scaled.png",2560,1665,false],"thumbnail":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-150x150.png",150,150,true],"medium":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-300x195.png",300,195,true],"medium_large":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-768x499.png",768,499,true],"large":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-1024x666.png",800,520,true],"1536x1536":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-1536x999.png",1536,999,true],"2048x2048":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-2048x1332.png",2048,1332,true],"onepress-blog-small":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-300x150.png",300,150,true],"onepress-small":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-480x300.png",480,300,true],"onepress-medium":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-640x400.png",640,400,true]},"uagb_author_info":{"display_name":"RCY","author_link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/author\/charlesy\/"},"uagb_comment_info":2,"uagb_excerpt":"$ conda config --add channels ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/5094","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/types\/post"}],"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=5094"}],"version-history":[{"count":10,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/5094\/revisions"}],"predecessor-version":[{"id":5108,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/5094\/revisions\/5108"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media\/5101"}],"wp:attachment":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media?parent=5094"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/categories?post=5094"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/tags?post=5094"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}xTB\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h2>\n
$ conda config --add channels conda-forge\n$ conda install xtb\n$ conda activate base<\/pre>\n\n\n
\u914d\u5ea7\u63a2\u7d22\u306e\u5b9f\u884c<\/h2>\n
45\n\nC -0.81100 -1.14800 -0.48800\nC -0.69700 -2.34500 -1.22600\nC -0.95300 -3.59200 -0.66600\nC -1.34200 -3.70100 0.66400\nC -1.44600 -2.52400 1.41300\nC -1.18300 -1.24800 0.89400\nC -1.34300 -0.32300 2.00500\nC -1.75000 -1.06700 3.09700\nN -1.81300 -2.37700 2.72900\nN -0.57600 0.04600 -1.16600\nC -1.73400 0.85100 -1.51900\nC 0.81000 0.55600 -1.30800\nC 1.09600 1.12200 -2.72000\nC 2.55800 1.57700 -2.84200\nC 0.82000 0.08600 -3.81700\nC 1.00000 1.61000 -0.18900\nO 0.88500 2.82200 -0.34800\nN 1.13800 1.01900 1.05800\nC 0.38400 1.56600 2.18200\nC -1.10500 1.16600 2.05200\nC 1.00800 1.11200 3.50900\nO 2.33200 1.63400 3.63300\nH -0.42000 -2.29200 -2.27700\nH -0.86300 -4.48600 -1.27800\nH -1.55500 -4.67200 1.10000\nH -1.98700 -0.76900 4.11000\nH -2.07500 -3.14200 3.33600\nH -2.15200 0.50500 -2.47000\nH -1.47500 1.90900 -1.63000\nH -2.52700 0.78900 -0.76700\nH 1.52300 -0.26100 -1.12300\nH 0.46200 1.99600 -2.91100\nH 3.24800 0.74700 -2.65500\nH 2.79300 2.37800 -2.13400\nH 2.76100 1.96400 -3.84700\nH 1.41300 -0.82200 -3.66200\nH 1.07400 0.48900 -4.80400\nH -0.23500 -0.19800 -3.84800\nH 1.26400 0.01200 1.06600\nH 0.45200 2.66000 2.12400\nH -1.53600 1.62600 1.15700\nH -1.66100 1.59400 2.89800\nH 1.08100 0.02200 3.57300\nH 0.42500 1.47300 4.36200\nH 2.71400 1.63300 2.73500<\/pre>\n
$ crest ILV.xyz -xnam xtb -gfn2 --gbsa h2o -niceprint -ewin 6 -T 18 > crest.out<\/pre>\n
\n \u2554\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2557\n \u2551 ___ ___ ___ ___ _____ \u2551\n \u2551 / __| _ \\ __/ __|_ _| \u2551\n \u2551 | (__| / _|\\__ \\ | | \u2551\n \u2551 \\___|_|_\\___|___/ |_| \u2551\n \u2551 \u2551\n \u2551 Conformer-Rotamer Ensemble Sampling Tool \u2551\n \u2551 based on the xTB methods \u2551\n \u2551 \u2551\n \u255a\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u255d\n Version 3.0.2, Sun, 25 August 20:02:44, 08/25/2024\n commit (af7eb99) compiled by 'usr@fv-az732-492'\n\n Cite work conducted with this code as\n\n \u2022 P.Pracht, F.Bohle, S.Grimme, PCCP, 2020, 22, 7169-7192.\n \u2022 S.Grimme, JCTC, 2019, 15, 2847-2862.\n \u2022 P.Pracht, S.Grimme, C.Bannwarth, F.Bohle, S.Ehlert,\n G.Feldmann, J.Gorges, M.M\u00fcller, T.Neudecker, C.Plett,\n S.Spicher, P.Steinbach, P.Weso\u0142owski, F.Zeller,\n J. Chem. Phys., 2024, 160, 114110.\n\n for works involving QCG cite\n\n \u2022 S.Spicher, C.Plett, P.Pracht, A.Hansen, S.Grimme,\n JCTC, 2022, 18 (5), 3174-3189.\n \u2022 C.Plett, S. Grimme,\n Angew. Chem. Int. Ed. 2023, 62, e202214477.\n\n for works involving MECP screening cite\n\n \u2022 P.Pracht, C.Bannwarth, JCTC, 2022, 18 (10), 6370-6385.\n\n Original code\n P.Pracht, S.Grimme, Universit\u00e4t Bonn, MCTC\n with help from (alphabetical order):\n C.Bannwarth, F.Bohle, S.Ehlert, G.Feldmann, J.Gorges,\n S.Grimme, C.Plett, P.Pracht, S.Spicher, P.Steinbach,\n P.Wesolowski, F.Zeller\n\n Online documentation is available at\n https://crest-lab.github.io/crest-docs/\n\n This program is distributed in the hope that it will be useful,\n but WITHOUT ANY WARRANTY; without even the implied warranty of\n MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n GNU Lesser General Public License (LGPL) for more details.\n\n Command line input:\n $ crest ILV.xyz -xnam xtb -gfn2 --gbsa h2o -niceprint -ewin 6 -T 14\n\n -xnam :\n xtb executable was set to: "xtb"\n --gfn2 : Use of GFN2-xTB requested.\n --gbsa h2o : implicit solvation\n -ewin 6\n -T 14 (CPUs/Threads selected)\n\n> Setting up backup calculator ... done.\n ----------------\n Calculation info\n ----------------\n> User-defined calculation level:\n : xTB calculation via tblite lib\n : GFN2-xTB level\n : Molecular charge : 0\n : Solvation model : gbsa\n : Solvent : h2o\n : Fermi temperature : 300.00000\n : Accuracy : 1.00000\n : max SCC cycles : 500\n\n\n -----------------------------\n Initial Geometry Optimization\n -----------------------------\n Geometry successfully optimized.\n\n \u250d\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2511\n \u2502 CREST iMTD-GC SAMPLING \u2502\n \u2515\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2519\n\n Input structure:\n 45\n\n C 0.1922437661 -1.4960850248 0.0897334052\n C 0.1765463882 -2.6657533739 -0.6543415539\n C 1.3295594653 -3.2493639719 -1.1744318231\n C 2.5606084738 -2.6770451414 -0.9517564360\n C 2.5945403662 -1.4854320276 -0.2377176468\n C 1.4331395855 -0.8412836507 0.2758770275\n C 1.8964937752 0.3888453894 0.8612729269\n C 3.2543375541 0.4085382022 0.7007920192\n N 3.6765632245 -0.7114941550 0.0538032076\n N -1.0528228940 -1.0836946587 0.6188187230\n C -1.1787274445 -0.9476079688 2.0525049206\n C -1.9511355590 -0.3331089640 -0.2470551535\n C -3.4306980816 -0.6721824436 -0.0296275657\n C -4.2845601548 0.1353496855 -1.0045996295\n C -3.6688215434 -2.1672177207 -0.2165686547\n C -1.6074850447 1.1167745115 0.0813008749\n O -2.2363729667 1.7982361301 0.8830666458\n N -0.4274856348 1.5248002587 -0.4571280921\n C 0.4535273222 2.3853694690 0.3185017027\n C 1.1306954393 1.5436404294 1.4254560819\n C 1.4667394510 3.0543306425 -0.6111273452\n O 0.8755041977 3.9949227158 -1.4755551157\n H -0.7763311441 -3.1484394964 -0.8078943880\n H 1.2511465285 -4.1694850641 -1.7336596417\n H 3.4696272194 -3.1242311862 -1.3228201397\n H 3.9477298023 1.1666291388 1.0086506145\n H 4.6292832413 -0.9324505017 -0.1806308990\n H -1.8417807629 -1.7271886071 2.4455576583\n H -1.5953145525 0.0204201959 2.3444377595\n H -0.2022700275 -1.0698724762 2.5199514383\n H -1.6782855227 -0.5653918746 -1.2818674551\n H -3.7010877085 -0.3839094088 0.9904693788\n H -4.0132778030 -0.0960479717 -2.0329186108\n H -4.1447163659 1.2008555427 -0.8383277713\n H -5.3368706205 -0.0977202351 -0.8640771554\n H -3.4354617237 -2.4597558056 -1.2385613186\n H -4.7101179143 -2.4085161108 -0.0186702232\n H -3.0435459024 -2.7419756406 0.4607845134\n H 0.0708404132 0.8313891623 -1.0015943253\n H -0.1748375933 3.1525879478 0.7826715116\n H 0.3487010001 1.2078930708 2.1068466172\n H 1.8139012173 2.1844731503 1.9841222489\n H 1.9973740977 2.2831782844 -1.1884513374\n H 2.1961422036 3.6109013681 -0.0196292060\n H 0.1289032220 3.5745789069 -1.9205507845\n\n ------------------------------------------------\n Generating MTD length from a flexibility measure\n ------------------------------------------------\n Calculating GFN0-xTB WBOs ... done.\n Calculating NCI flexibility ... done.\n covalent flexibility measure : 0.228\n non-covalent flexibility measure : 0.688\n flexibility measure : 0.278\n t(MTD) / ps : 8.0\n \u03a3(t(MTD)) / ps : 112.0 (14 MTDs)\n\n -----------------------------------\n Starting trial MTD to test settings\n -----------------------------------\n Trial MTD 1 runtime (1.0 ps) ... 0 min, 11.723 sec\n Estimated runtime for one MTD (8.0 ps) on a single thread: 1 min 34 sec\n Estimated runtime for a batch of 14 MTDs on 14 threads: 1 min 34 sec\n\n******************************************************************************************\n** N E W I T E R A T I O N C Y C L E **\n******************************************************************************************\n\n ------------------------------\n Meta-Dynamics Iteration 1\n ------------------------------\n list of applied metadynamics Vbias parameters:\n$metadyn 0.13500 1.300\n$metadyn 0.06750 1.300\n$metadyn 0.03375 1.300\n$metadyn 0.13500 0.780\n$metadyn 0.06750 0.780\n$metadyn 0.03375 0.780\n$metadyn 0.13500 0.468\n$metadyn 0.06750 0.468\n$metadyn 0.03375 0.468\n$metadyn 0.13500 0.281\n$metadyn 0.06750 0.281\n$metadyn 0.03375 0.281\n$metadyn 0.04500 0.100\n$metadyn 0.22500 0.800\n\n ::::::::::::: starting MTD 8 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0675 Eh |\n | Vbias exponent (\u03b1) : 0.4680 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 11 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0675 Eh |\n | Vbias exponent (\u03b1) : 0.2808 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 9 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0338 Eh |\n | Vbias exponent (\u03b1) : 0.4680 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 14 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.2250 Eh |\n | Vbias exponent (\u03b1) : 0.8000 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 7 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.1350 Eh |\n | Vbias exponent (\u03b1) : 0.4680 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 13 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0450 Eh |\n | Vbias exponent (\u03b1) : 0.1000 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 2 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0675 Eh |\n | Vbias exponent (\u03b1) : 1.3000 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 5 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0675 Eh |\n | Vbias exponent (\u03b1) : 0.7800 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 6 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0338 Eh |\n | Vbias exponent (\u03b1) : 0.7800 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 10 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.1350 Eh |\n | Vbias exponent (\u03b1) : 0.2808 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 3 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0338 Eh |\n | Vbias exponent (\u03b1) : 1.3000 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 12 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0338 Eh |\n | Vbias exponent (\u03b1) : 0.2808 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 1 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.1350 Eh |\n | Vbias exponent (\u03b1) : 1.3000 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 4 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.1350 Eh |\n | Vbias exponent (\u03b1) : 0.7800 bohr\u207b\u00b2 |\n*MTD 4 completed successfully ... 2 min, 0.580 sec\n*MTD 3 completed successfully ... 2 min, 0.981 sec\n*MTD 1 completed successfully ... 2 min, 1.238 sec\n*MTD 12 completed successfully ... 2 min, 1.282 sec\n*MTD 5 completed successfully ... 2 min, 1.477 sec\n*MTD 11 completed successfully ... 2 min, 1.821 sec\n*MTD 7 completed successfully ... 2 min, 1.977 sec\n*MTD 14 completed successfully ... 2 min, 2.063 sec\n*MTD 13 completed successfully ... 2 min, 2.065 sec\n*MTD 8 completed successfully ... 2 min, 2.211 sec\n*MTD 10 completed successfully ... 2 min, 2.409 sec\n*MTD 6 completed successfully ... 2 min, 2.656 sec\n*MTD 9 completed successfully ... 2 min, 2.692 sec\n*MTD 2 completed successfully ... 2 min, 2.859 sec\n\n ======================================\n | Multilevel Ensemble Optimization |\n ======================================\n Optimizing all 1106 structures from file "crest_dynamics.trj" ...\n ----------------------\n crude pre-optimization\n ----------------------\n Optimization engine: ANCOPT\n Hessian update type: BFGS\n E/G convergence criteria: 0.500E-03 Eh, 0.100E-01 Eh/a0\n maximum optimization steps: 200\n |>0.1% |>7.5% |>15.0% |>22.5% |>30.0% |>37.5% |>45.0% |>52.5% |>60.0% |>67.5% |>75.0% |>82.5% |>90.1% |>97.6% |>100.0%\n done.\n> 1106 of 1106 structures successfully optimized (100.0% success)\n> Total runtime for 1106 optimizations:\n * wall-time: 0 d, 0 h, 1 min, 35.498 sec\n * cpu-time: 0 d, 0 h, 22 min, 6.834 sec\n * ratio c/w: 13.894 speedup\n> Corresponding to approximately 0.086 sec per processed structure\n\nCREGEN> running RMSDs ... done.\nCREGEN> E lowest : -65.09755\n 729 structures remain within 12.00 kcal/mol window\n ----------------------------------\n optimization with tight thresholds\n ----------------------------------\n Optimization engine: ANCOPT\n Hessian update type: BFGS\n E/G convergence criteria: 0.100E-05 Eh, 0.800E-03 Eh/a0\n maximum optimization steps: 200\n |>0.1% |>10.0% |>20.0% |>30.0% |>40.1% |>50.1% |>60.1% |>70.1% |>80.1% |>90.1% |>100.0%\n done.\n> 729 of 729 structures successfully optimized (100.0% success)\n> Total runtime for 729 optimizations:\n * wall-time: 0 d, 0 h, 1 min, 26.478 sec\n * cpu-time: 0 d, 0 h, 19 min, 54.857 sec\n * ratio c/w: 13.817 speedup\n> Corresponding to approximately 0.119 sec per processed structure\n\nCREGEN> running RMSDs ... done.\nCREGEN> E lowest : -65.09784\n 122 structures remain within 6.00 kcal/mol window\n\n ------------------------------\n Meta-Dynamics Iteration 2\n ------------------------------\n list of applied metadynamics Vbias parameters:\n$metadyn 0.13500 1.300\n$metadyn 0.06750 1.300\n$metadyn 0.03375 1.300\n$metadyn 0.13500 0.780\n$metadyn 0.06750 0.780\n$metadyn 0.03375 0.780\n$metadyn 0.13500 0.468\n$metadyn 0.06750 0.468\n$metadyn 0.03375 0.468\n$metadyn 0.13500 0.281\n$metadyn 0.06750 0.281\n$metadyn 0.03375 0.281\n$metadyn 0.04500 0.100\n$metadyn 0.22500 0.800\n\n ::::::::::::: starting MTD 10 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.1350 Eh |\n | Vbias exponent (\u03b1) : 0.2808 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 6 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0338 Eh |\n | Vbias exponent (\u03b1) : 0.7800 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 5 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0675 Eh |\n | Vbias exponent (\u03b1) : 0.7800 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 3 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0338 Eh |\n | Vbias exponent (\u03b1) : 1.3000 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 2 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0675 Eh |\n | Vbias exponent (\u03b1) : 1.3000 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 8 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0675 Eh |\n | Vbias exponent (\u03b1) : 0.4680 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 9 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0338 Eh |\n | Vbias exponent (\u03b1) : 0.4680 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 1 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.1350 Eh |\n | Vbias exponent (\u03b1) : 1.3000 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 11 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0675 Eh |\n | Vbias exponent (\u03b1) : 0.2808 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 13 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0450 Eh |\n | Vbias exponent (\u03b1) : 0.1000 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 4 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.1350 Eh |\n | Vbias exponent (\u03b1) : 0.7800 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 7 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.1350 Eh |\n | Vbias exponent (\u03b1) : 0.4680 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 14 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.2250 Eh |\n | Vbias exponent (\u03b1) : 0.8000 bohr\u207b\u00b2 |\n ::::::::::::: starting MTD 12 :::::::::::::\n | MD simulation time : 8.0 ps |\n | target T : 300.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n | dump interval(Vbias) : 1.00 ps |\n | Vbias prefactor (k) : 0.0338 Eh |\n | Vbias exponent (\u03b1) : 0.2808 bohr\u207b\u00b2 |\n*MTD 4 completed successfully ... 2 min, 0.400 sec\n*MTD 7 completed successfully ... 2 min, 0.479 sec\n*MTD 5 completed successfully ... 2 min, 0.911 sec\n*MTD 8 completed successfully ... 2 min, 1.311 sec\n*MTD 12 completed successfully ... 2 min, 1.473 sec\n*MTD 2 completed successfully ... 2 min, 1.540 sec\n*MTD 10 completed successfully ... 2 min, 1.569 sec\n*MTD 11 completed successfully ... 2 min, 1.932 sec\n*MTD 1 completed successfully ... 2 min, 2.180 sec\n*MTD 6 completed successfully ... 2 min, 2.344 sec\n*MTD 14 completed successfully ... 2 min, 2.349 sec\n*MTD 9 completed successfully ... 2 min, 2.604 sec\n*MTD 3 completed successfully ... 2 min, 2.632 sec\n*MTD 13 completed successfully ... 2 min, 2.883 sec\n\n ======================================\n | Multilevel Ensemble Optimization |\n ======================================\n Optimizing all 1106 structures from file "crest_dynamics.trj" ...\n ----------------------\n crude pre-optimization\n ----------------------\n Optimization engine: ANCOPT\n Hessian update type: BFGS\n E/G convergence criteria: 0.500E-03 Eh, 0.100E-01 Eh/a0\n maximum optimization steps: 200\n |>0.1% |>7.5% |>15.0% |>22.5% |>30.0% |>37.5% |>45.0% |>52.5% |>60.0% |>67.5% |>75.0% |>82.5% |>90.1% |>97.6% |>100.0%\n done.\n> 1106 of 1106 structures successfully optimized (100.0% success)\n> Total runtime for 1106 optimizations:\n * wall-time: 0 d, 0 h, 1 min, 38.800 sec\n * cpu-time: 0 d, 0 h, 22 min, 46.570 sec\n * ratio c/w: 13.832 speedup\n> Corresponding to approximately 0.089 sec per processed structure\n\nCREGEN> running RMSDs ... done.\nCREGEN> E lowest : -65.09606\n 776 structures remain within 12.00 kcal/mol window\n ----------------------------------\n optimization with tight thresholds\n ----------------------------------\n Optimization engine: ANCOPT\n Hessian update type: BFGS\n E/G convergence criteria: 0.100E-05 Eh, 0.800E-03 Eh/a0\n maximum optimization steps: 200\n |>0.1% |>10.1% |>20.1% |>30.0% |>40.1% |>50.0% |>60.1% |>70.1% |>80.0% |>90.1% |>100.0%\n done.\n> 776 of 776 structures successfully optimized (100.0% success)\n> Total runtime for 776 optimizations:\n * wall-time: 0 d, 0 h, 1 min, 34.821 sec\n * cpu-time: 0 d, 0 h, 21 min, 46.152 sec\n * ratio c/w: 13.775 speedup\n> Corresponding to approximately 0.122 sec per processed structure\n\nCREGEN> running RMSDs ... done.\nCREGEN> E lowest : -65.09630\n 150 structures remain within 6.00 kcal/mol window\n\n========================================\n MTD Simulations done \n========================================\n Collecting ensmbles.\nCREGEN> running RMSDs ... done.\nCREGEN> E lowest : -65.09784\n 182 structures remain within 6.00 kcal/mol window\n\n\n ===============================================\n Additional regular MDs on lowest 4 conformer(s)\n ===============================================\n :::::::::::::: starting MD 1 ::::::::::::::\n | MD simulation time : 4.0 ps |\n | target T : 400.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n :::::::::::::: starting MD 8 ::::::::::::::\n | MD simulation time : 4.0 ps |\n | target T : 500.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n :::::::::::::: starting MD 6 ::::::::::::::\n | MD simulation time : 4.0 ps |\n | target T : 500.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n :::::::::::::: starting MD 2 ::::::::::::::\n | MD simulation time : 4.0 ps |\n | target T : 400.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n :::::::::::::: starting MD 3 ::::::::::::::\n | MD simulation time : 4.0 ps |\n | target T : 400.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n :::::::::::::: starting MD 5 ::::::::::::::\n | MD simulation time : 4.0 ps |\n | target T : 500.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n :::::::::::::: starting MD 4 ::::::::::::::\n | MD simulation time : 4.0 ps |\n | target T : 400.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n :::::::::::::: starting MD 7 ::::::::::::::\n | MD simulation time : 4.0 ps |\n | target T : 500.0 K |\n | timestep dt : 5.0 fs |\n | dump interval(trj) : 100.0 fs |\n | SHAKE algorithm : true (all bonds) |\n*MD 1 completed successfully ... 0 min, 54.351 sec\n*MD 4 completed successfully ... 0 min, 54.539 sec\n*MD 5 completed successfully ... 0 min, 54.938 sec\n*MD 2 completed successfully ... 0 min, 54.984 sec\n*MD 7 completed successfully ... 0 min, 54.993 sec\n*MD 8 completed successfully ... 0 min, 55.006 sec\n*MD 6 completed successfully ... 0 min, 55.034 sec\n*MD 3 completed successfully ... 0 min, 55.062 sec\n Appending file crest_rotamers_1.xyz with new structures\n Optimizing all 494 structures from file "crest_rotamers_1.xyz" ...\n ----------------------------------\n optimization with tight thresholds\n ----------------------------------\n Optimization engine: ANCOPT\n Hessian update type: BFGS\n E/G convergence criteria: 0.100E-05 Eh, 0.800E-03 Eh/a0\n maximum optimization steps: 200\n |>0.2% |>10.1% |>20.0% |>30.2% |>40.1% |>50.0% |>60.1% |>70.0% |>80.2% |>90.1% |>100.0%\n done.\n> 494 of 494 structures successfully optimized (100.0% success)\n> Total runtime for 494 optimizations:\n * wall-time: 0 d, 0 h, 0 min, 45.615 sec\n * cpu-time: 0 d, 0 h, 10 min, 19.974 sec\n * ratio c/w: 13.592 speedup\n> Corresponding to approximately 0.092 sec per processed structure\n\nCREGEN> running RMSDs ... done.\nCREGEN> E lowest : -65.09785\n 211 structures remain within 6.00 kcal/mol window\n\n ========================================\n | Structure Crossing (GC) |\n ========================================\n\n =============================\n # threads = 14\n =============================\ninput file name : crest_rotamers_2.xyz\nnumber of atoms : 45\nnumber of points on xyz files : 211\nconformer energy window /kcal : 6.00\nCN per atom difference cut-off : 0.3000\nRMSD threshold (Ang, Bohr) : 0.2500 0.4724\nmax. # of generated structures : 400\n # in E window 211\n 10.2 % done\n 35.2 % done\n 60.3 % done\n finished.\n average rmsd w.r.t input : 1.61661\n number of clash discarded : 11478\n removed identical structures : 9136\n\n 400 structures written to confcross.xyz\n\n\n ======================================\n | Multilevel Ensemble Optimization |\n ======================================\n Optimizing all 400 structures from file "confcross.xyz" ...\n ----------------------\n crude pre-optimization\n ----------------------\n Optimization engine: ANCOPT\n Hessian update type: BFGS\n E/G convergence criteria: 0.500E-03 Eh, 0.100E-01 Eh/a0\n maximum optimization steps: 200\n |>0.2% |>10.0% |>20.0% |>30.0% |>40.0% |>50.0% |>60.0% |>70.2% |>80.0% |>90.2% |>100.0%\n done.\n> 400 of 400 structures successfully optimized (100.0% success)\n> Total runtime for 400 optimizations:\n * wall-time: 0 d, 0 h, 0 min, 17.123 sec\n * cpu-time: 0 d, 0 h, 3 min, 55.314 sec\n * ratio c/w: 13.743 speedup\n> Corresponding to approximately 0.043 sec per processed structure\n\nCREGEN> running RMSDs ... done.\nCREGEN> E lowest : -65.09782\n 96 structures remain within 12.00 kcal/mol window\n ----------------------------------\n optimization with tight thresholds\n ----------------------------------\n Optimization engine: ANCOPT\n Hessian update type: BFGS\n E/G convergence criteria: 0.100E-05 Eh, 0.800E-03 Eh/a0\n maximum optimization steps: 200\n |>1.0% |>10.4% |>20.8% |>30.2% |>40.6% |>50.0% |>60.4% |>70.8% |>80.2% |>90.6% |>100.0%\n done.\n> 96 of 96 structures successfully optimized (100.0% success)\n> Total runtime for 96 optimizations:\n * wall-time: 0 d, 0 h, 0 min, 6.321 sec\n * cpu-time: 0 d, 0 h, 1 min, 23.505 sec\n * ratio c/w: 13.211 speedup\n> Corresponding to approximately 0.066 sec per processed structure\n\nCREGEN> running RMSDs ... done.\nCREGEN> E lowest : -65.09784\n 64 structures remain within 6.00 kcal/mol window\nappending new structures to crest_rotamers_2.xyz\nCREGEN> running RMSDs ... done.\nCREGEN> E lowest : -65.09785\n\n\n ================================================\n | Final Geometry Optimization |\n ================================================\n Optimizing all 265 structures from file "crest_rotamers_3.xyz" ...\n ---------------------------------------\n optimization with very tight thresholds\n ---------------------------------------\n Optimization engine: ANCOPT\n Hessian update type: BFGS\n E/G convergence criteria: 0.100E-06 Eh, 0.200E-03 Eh/a0\n maximum optimization steps: 200\n |>0.4% |>10.2% |>20.0% |>30.2% |>40.0% |>50.2% |>60.0% |>70.2% |>80.0% |>90.2% |>100.0%\n done.\n> 265 of 265 structures successfully optimized (100.0% success)\n> Total runtime for 265 optimizations:\n * wall-time: 0 d, 0 h, 0 min, 8.178 sec\n * cpu-time: 0 d, 0 h, 1 min, 50.809 sec\n * ratio c/w: 13.550 speedup\n> Corresponding to approximately 0.031 sec per processed structure\n\nCREGEN> running RMSDs ... done.\nCREGEN> E lowest : -65.09784\n 265 structures remain within 6.00 kcal/mol window\n\n\n --------------------------\n Final Ensemble Information\n --------------------------\n input file name : crest_rotamers_3.xyz\n output file name : crest_rotamers_4.xyz\n number of atoms : 45\n number of points on xyz files : 265\n RMSD threshold : 0.1250\n Bconst threshold : 0.0100\n population threshold : 0.0500\n # fragment in coord : 1\n # bonds in reference structure : 47\n number of reliable points : 265\n sorting energy window (EWIN) : 6.0000 / kcal*mol\u207b\u00b9\n reference state Etot : -65.097837880000000\n number of doubles removed by rot/RMSD : 0\n total number unique points considered further : 265\n Erel/kcal Etot weight/tot conformer set degen origin\n 1 0.000 -65.09784 0.05480 0.82181 1 15\n 2 0.000 -65.09784 0.05479\n 3 0.000 -65.09784 0.05479\n 4 0.000 -65.09784 0.05479\n 5 0.000 -65.09784 0.05479\n 6 0.000 -65.09784 0.05479\n 7 0.000 -65.09784 0.05479\n 8 0.000 -65.09784 0.05479\n 9 0.000 -65.09784 0.05479\n 10 0.000 -65.09784 0.05478\n 11 0.000 -65.09784 0.05478\n 12 0.000 -65.09784 0.05478\n 13 0.000 -65.09784 0.05478\n 14 0.000 -65.09784 0.05478\n 15 0.000 -65.09784 0.05477\n 16 0.966 -65.09630 0.01075 0.05373 2 5\n 17 0.966 -65.09630 0.01075\n 18 0.966 -65.09630 0.01075\n 19 0.966 -65.09630 0.01075\n 20 0.966 -65.09630 0.01074\n 21 1.300 -65.09577 0.00612 0.03058 3 5\n 22 1.300 -65.09577 0.00612\n 23 1.300 -65.09577 0.00612\n 24 1.300 -65.09577 0.00612\n 25 1.300 -65.09577 0.00612\n 26 1.741 -65.09506 0.00291 0.02906 4 10\n 27 1.741 -65.09506 0.00291\n 28 1.741 -65.09506 0.00291\n 29 1.741 -65.09506 0.00291\n 30 1.741 -65.09506 0.00291\n 31 1.741 -65.09506 0.00291\n 32 1.742 -65.09506 0.00291\n 33 1.742 -65.09506 0.00291\n 34 1.742 -65.09506 0.00291\n 35 1.742 -65.09506 0.00291\n 36 1.810 -65.09495 0.00259 0.03109 5 12\n 37 1.810 -65.09495 0.00259\n 38 1.810 -65.09495 0.00259\n 39 1.810 -65.09495 0.00259\n 40 1.810 -65.09495 0.00259\n 41 1.810 -65.09495 0.00259\n 42 1.810 -65.09495 0.00259\n 43 1.810 -65.09495 0.00259\n 44 1.810 -65.09495 0.00259\n 45 1.810 -65.09495 0.00259\n 46 1.810 -65.09495 0.00259\n 47 1.810 -65.09495 0.00259\n 48 1.871 -65.09486 0.00234 0.01401 6 6\n 49 1.871 -65.09486 0.00234\n 50 1.871 -65.09486 0.00234\n 51 1.871 -65.09486 0.00234\n 52 1.871 -65.09486 0.00234\n 53 1.871 -65.09486 0.00234\n 54 2.104 -65.09448 0.00158 0.00946 7 6\n 55 2.104 -65.09448 0.00158\n 56 2.104 -65.09448 0.00158\n 57 2.104 -65.09448 0.00158\n 58 2.104 -65.09448 0.00158\n 59 2.104 -65.09448 0.00158\n 60 2.197 -65.09434 0.00135 0.00539 8 4\n 61 2.197 -65.09434 0.00135\n 62 2.197 -65.09434 0.00135\n 63 2.197 -65.09434 0.00135\n 64 3.259 -65.09264 0.00022 0.00045 9 2\n 65 3.259 -65.09264 0.00022\n 66 3.348 -65.09250 0.00019 0.00058 10 3\n 67 3.348 -65.09250 0.00019\n 68 3.348 -65.09250 0.00019\n 69 3.729 -65.09190 0.00010 0.00020 11 2\n 70 3.729 -65.09190 0.00010\n 71 3.927 -65.09158 0.00007 0.00058 12 8\n 72 3.927 -65.09158 0.00007\n 73 3.927 -65.09158 0.00007\n 74 3.927 -65.09158 0.00007\n 75 3.927 -65.09158 0.00007\n 76 3.927 -65.09158 0.00007\n 77 3.927 -65.09158 0.00007\n 78 3.927 -65.09158 0.00007\n 79 4.363 -65.09089 0.00003 0.00035 13 10\n 80 4.363 -65.09089 0.00003\n 81 4.363 -65.09089 0.00003\n 82 4.363 -65.09089 0.00003\n 83 4.363 -65.09089 0.00003\n 84 4.363 -65.09089 0.00003\n 85 4.363 -65.09089 0.00003\n 86 4.363 -65.09088 0.00003\n 87 4.363 -65.09088 0.00003\n 88 4.363 -65.09088 0.00003\n 89 4.389 -65.09084 0.00003 0.00013 14 4\n 90 4.389 -65.09084 0.00003\n 91 4.389 -65.09084 0.00003\n 92 4.389 -65.09084 0.00003\n 93 4.424 -65.09079 0.00003 0.00060 15 19\n 94 4.424 -65.09079 0.00003\n 95 4.424 -65.09079 0.00003\n 96 4.424 -65.09079 0.00003\n 97 4.424 -65.09079 0.00003\n 98 4.424 -65.09079 0.00003\n 99 4.424 -65.09079 0.00003\n 100 4.424 -65.09079 0.00003\n 101 4.424 -65.09079 0.00003\n 102 4.424 -65.09079 0.00003\n 103 4.424 -65.09079 0.00003\n 104 4.424 -65.09079 0.00003\n 105 4.424 -65.09079 0.00003\n 106 4.424 -65.09079 0.00003\n 107 4.424 -65.09079 0.00003\n 108 4.424 -65.09079 0.00003\n 109 4.424 -65.09079 0.00003\n 110 4.424 -65.09079 0.00003\n 111 4.424 -65.09079 0.00003\n 112 4.514 -65.09064 0.00003 0.00073 16 27\n 113 4.514 -65.09064 0.00003\n 114 4.514 -65.09064 0.00003\n 115 4.514 -65.09064 0.00003\n 116 4.514 -65.09064 0.00003\n 117 4.514 -65.09064 0.00003\n 118 4.514 -65.09064 0.00003\n 119 4.514 -65.09064 0.00003\n 120 4.514 -65.09064 0.00003\n 121 4.514 -65.09064 0.00003\n 122 4.514 -65.09064 0.00003\n 123 4.514 -65.09064 0.00003\n 124 4.514 -65.09064 0.00003\n 125 4.514 -65.09064 0.00003\n 126 4.514 -65.09064 0.00003\n 127 4.514 -65.09064 0.00003\n 128 4.514 -65.09064 0.00003\n 129 4.514 -65.09064 0.00003\n 130 4.514 -65.09064 0.00003\n 131 4.514 -65.09064 0.00003\n 132 4.514 -65.09064 0.00003\n 133 4.514 -65.09064 0.00003\n 134 4.514 -65.09064 0.00003\n 135 4.514 -65.09064 0.00003\n 136 4.514 -65.09064 0.00003\n 137 4.514 -65.09064 0.00003\n 138 4.514 -65.09064 0.00003\n 139 4.540 -65.09060 0.00003 0.00054 17 21\n 140 4.540 -65.09060 0.00003\n 141 4.540 -65.09060 0.00003\n 142 4.540 -65.09060 0.00003\n 143 4.540 -65.09060 0.00003\n 144 4.540 -65.09060 0.00003\n 145 4.540 -65.09060 0.00003\n 146 4.540 -65.09060 0.00003\n 147 4.540 -65.09060 0.00003\n 148 4.540 -65.09060 0.00003\n 149 4.540 -65.09060 0.00003\n 150 4.540 -65.09060 0.00003\n 151 4.540 -65.09060 0.00003\n 152 4.540 -65.09060 0.00003\n 153 4.540 -65.09060 0.00003\n 154 4.540 -65.09060 0.00003\n 155 4.540 -65.09060 0.00003\n 156 4.540 -65.09060 0.00003\n 157 4.540 -65.09060 0.00003\n 158 4.540 -65.09060 0.00003\n 159 4.540 -65.09060 0.00003\n 160 4.682 -65.09038 0.00002 0.00004 18 2\n 161 4.682 -65.09038 0.00002\n 162 4.785 -65.09021 0.00002 0.00002 19 1\n 163 4.892 -65.09004 0.00001 0.00001 20 1\n 164 4.927 -65.08999 0.00001 0.00015 21 11\n 165 4.927 -65.08999 0.00001\n 166 4.927 -65.08999 0.00001\n 167 4.927 -65.08999 0.00001\n 168 4.927 -65.08999 0.00001\n 169 4.927 -65.08999 0.00001\n 170 4.927 -65.08999 0.00001\n 171 4.928 -65.08999 0.00001\n 172 4.928 -65.08999 0.00001\n 173 4.928 -65.08999 0.00001\n 174 4.928 -65.08999 0.00001\n 175 4.966 -65.08992 0.00001 0.00001 22 1\n 176 5.041 -65.08980 0.00001 0.00004 23 4\n 177 5.041 -65.08980 0.00001\n 178 5.041 -65.08980 0.00001\n 179 5.041 -65.08980 0.00001\n 180 5.097 -65.08971 0.00001 0.00002 24 2\n 181 5.097 -65.08971 0.00001\n 182 5.101 -65.08971 0.00001 0.00002 25 2\n 183 5.101 -65.08971 0.00001\n 184 5.193 -65.08956 0.00001 0.00011 26 13\n 185 5.193 -65.08956 0.00001\n 186 5.193 -65.08956 0.00001\n 187 5.193 -65.08956 0.00001\n 188 5.193 -65.08956 0.00001\n 189 5.193 -65.08956 0.00001\n 190 5.193 -65.08956 0.00001\n 191 5.193 -65.08956 0.00001\n 192 5.193 -65.08956 0.00001\n 193 5.193 -65.08956 0.00001\n 194 5.193 -65.08956 0.00001\n 195 5.193 -65.08956 0.00001\n 196 5.193 -65.08956 0.00001\n 197 5.333 -65.08934 0.00001 0.00001 27 1\n 198 5.520 -65.08904 0.00000 0.00000 28 1\n 199 5.536 -65.08902 0.00000 0.00001 29 2\n 200 5.536 -65.08902 0.00000\n 201 5.538 -65.08901 0.00000 0.00011 30 23\n 202 5.538 -65.08901 0.00000\n 203 5.538 -65.08901 0.00000\n 204 5.538 -65.08901 0.00000\n 205 5.538 -65.08901 0.00000\n 206 5.538 -65.08901 0.00000\n 207 5.538 -65.08901 0.00000\n 208 5.538 -65.08901 0.00000\n 209 5.538 -65.08901 0.00000\n 210 5.538 -65.08901 0.00000\n 211 5.538 -65.08901 0.00000\n 212 5.538 -65.08901 0.00000\n 213 5.538 -65.08901 0.00000\n 214 5.538 -65.08901 0.00000\n 215 5.538 -65.08901 0.00000\n 216 5.538 -65.08901 0.00000\n 217 5.538 -65.08901 0.00000\n 218 5.538 -65.08901 0.00000\n 219 5.538 -65.08901 0.00000\n 220 5.538 -65.08901 0.00000\n 221 5.538 -65.08901 0.00000\n 222 5.538 -65.08901 0.00000\n 223 5.538 -65.08901 0.00000\n 224 5.642 -65.08885 0.00000 0.00000 31 1\n 225 5.802 -65.08859 0.00000 0.00006 32 21\n 226 5.802 -65.08859 0.00000\n 227 5.802 -65.08859 0.00000\n 228 5.802 -65.08859 0.00000\n 229 5.802 -65.08859 0.00000\n 230 5.802 -65.08859 0.00000\n 231 5.802 -65.08859 0.00000\n 232 5.802 -65.08859 0.00000\n 233 5.802 -65.08859 0.00000\n 234 5.802 -65.08859 0.00000\n 235 5.802 -65.08859 0.00000\n 236 5.802 -65.08859 0.00000\n 237 5.802 -65.08859 0.00000\n 238 5.802 -65.08859 0.00000\n 239 5.802 -65.08859 0.00000\n 240 5.802 -65.08859 0.00000\n 241 5.802 -65.08859 0.00000\n 242 5.802 -65.08859 0.00000\n 243 5.802 -65.08859 0.00000\n 244 5.802 -65.08859 0.00000\n 245 5.802 -65.08859 0.00000\n 246 5.881 -65.08847 0.00000 0.00005 33 20\n 247 5.881 -65.08847 0.00000\n 248 5.881 -65.08847 0.00000\n 249 5.881 -65.08847 0.00000\n 250 5.881 -65.08847 0.00000\n 251 5.881 -65.08847 0.00000\n 252 5.881 -65.08847 0.00000\n 253 5.881 -65.08847 0.00000\n 254 5.881 -65.08847 0.00000\n 255 5.881 -65.08847 0.00000\n 256 5.881 -65.08847 0.00000\n 257 5.881 -65.08847 0.00000\n 258 5.881 -65.08847 0.00000\n 259 5.881 -65.08847 0.00000\n 260 5.881 -65.08847 0.00000\n 261 5.881 -65.08847 0.00000\n 262 5.881 -65.08847 0.00000\n 263 5.881 -65.08847 0.00000\n 264 5.881 -65.08847 0.00000\n 265 5.881 -65.08847 0.00000\nT /K : 298.15\nE lowest : -65.09784\nensemble average energy (kcal) : 0.277\nensemble entropy (J/mol K, cal/mol K) : 28.033 6.700\nensemble free energy (kcal/mol) : -1.998\npopulation of lowest in % : 82.181\n number of unique conformers for further calc 33\n list of relative energies saved as "crest.energies"\n\n -----------------\n Wall Time Summary\n -----------------\n CREST runtime (total) 0 d, 0 h, 12 min, 54.649 sec\n ------------------------------------------------------------------\n Trial metadynamics (MTD) ... 0 min, 11.726 sec ( 1.514%)\n Metadynamics (MTD) ... 4 min, 7.803 sec ( 31.989%)\n Geometry optimization ... 7 min, 14.403 sec ( 56.077%)\n Molecular dynamics (MD) ... 0 min, 55.106 sec ( 7.114%)\n Genetic crossing (GC) ... 0 min, 24.307 sec ( 3.138%)\n I/O and setup ... 0 min, 1.304 sec ( 0.168%)\n ------------------------------------------------------------------\n * wall-time: 0 d, 0 h, 12 min, 54.649 sec\n * cpu-time: 0 d, 2 h, 49 min, 10.989 sec\n * ratio c/w: 13.104 speedup\n ------------------------------------------------------------------\n * Total number of energy+grad calls: 148615\n\n CREST terminated normally.\n<\/pre>\n\n\n\n
\u7d50\u679c<\/h2>\n
![\"\"](\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2025\/08\/Screenshot-2025-08-06-at-12.41.43-PM-1024x666.png\")
<\/p>\n