{"id":2459,"date":"2023-09-19T17:00:09","date_gmt":"2023-09-19T21:00:09","guid":{"rendered":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/?page_id=2459"},"modified":"2024-10-14T14:01:39","modified_gmt":"2024-10-14T18:01:39","slug":"manual-of-gamd-in-genesis","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/manual-of-gamd-in-genesis\/","title":{"rendered":"GaMD-GENESIS: Manual"},"content":{"rendered":"<h2>Simulation Parameter Settings<\/h2>\n<p class=\"body\"><strong>gamd<\/strong> YES \/ NO<br \/>\nDefault : NO<br \/>\nEnable the GaMD method.<\/p>\n<p class=\"body\"><strong>boost<\/strong> YES \/ NO<br \/>\nDefault : YES<br \/>\nFlag to apply GaMD boost to the system. If boost = NO, boost is not applied but GaMD parameters are updated from the trajectory.<\/p>\n<p class=\"body\"><strong>boost_type<\/strong> DUAL \/ DIHEDRAL \/ POTENTIAL<br \/>\nDefault: DUAL<br \/>\nType of boost.<br \/>\nDUAL: Boost is applied on both the dihedral and total potential energies.<br \/>\nDIHEDRAL: Boost is applied on only the dihedral energy.<br \/>\nPOTENTIAL: Boost is applied on only the total potential energy.<\/p>\n<p class=\"body\"><strong>thresh_type<\/strong> LOWER \/ HIGHER<br \/>\nDefault: LOWER Type of threshold.<br \/>\nLOWER: E is set to the lower bound E = Umax.<br \/>\nHIGHER: E is set to its upper bound E = Umin + 1\/k.<\/p>\n<p class=\"body\"><strong>update_period<\/strong> Integer<br \/>\nDefault: 0<br \/>\nPeriod of updating parameters in units of time step.<\/p>\n<p class=\"body\"><strong>sigma0_pot<\/strong> Real<br \/>\nDefault: 6.0 (unit: kcal\/mol)<br \/>\nUpper limit of the standard deviation of the total potential boost that allows for accurate reweighting.<\/p>\n<p class=\"body\"><strong>pot_max<\/strong> Real<br \/>\nDefault: -99999999.0 (unit: kcal\/mol)<br \/>\nMaximum of the total potential energy of the system.<\/p>\n<p class=\"body\"><strong>pot_min<\/strong> Real<br \/>\nDefault: 99999999.0 (unit: kcal\/mol)<br \/>\nMinimum of the total potential energy of the system.<\/p>\n<p class=\"body\"><strong>pot_ave<\/strong> Real<br \/>\nDefault: 0.0 (unit: kcal\/mol)<br \/>\nAverage of the total potential energy of the system.<\/p>\n<p class=\"body\"><strong>pot_dev<\/strong> Real<br \/>\nDefault: 0.0 (unit: kcal\/mol)<br \/>\nStandard deviation of the total potential energy of the system.<\/p>\n<p class=\"body\"><strong>sigma0_dih<\/strong> Real<br \/>\nDefault: 6.0 (unit: kcal\/mol)<br \/>\nUpper limit of the standard deviation of the dihedral boost that allows for accurate reweighting.<\/p>\n<p class=\"body\"><strong>dih_max<\/strong> Real<br \/>\nDefault: -99999999.0 (unit: kcal\/mol)<br \/>\nMaximum of the dihedral energy of the system.<\/p>\n<p class=\"body\"><strong>dih_min<\/strong> Real<br \/>\nDefault: 99999999.0 (unit: kcal\/mol)<br \/>\nMinimum of the dihedral energy of the system.<\/p>\n<p class=\"body\"><strong>dih_ave<\/strong> Real<br \/>\nDefault: 0.0 (unit: kcal\/mol)<br \/>\nAverage of the dihedral energy of the system.<\/p>\n<p class=\"body\"><strong>dih_dev<\/strong> Real<br \/>\nDefault: 0.0 (unit: kcal\/mol)<br \/>\nStandard deviation of the dihedral energy of the system.<\/p>\n<p class=\"body\">NOTE: Please refer to the <a href=\"https:\/\/www.r-ccs.riken.jp\/labs\/cbrt\/?smd_process_download=1&amp;download_id=13809\" rel=\"noopener\">GENESIS user manual<\/a> for more detailed description.<\/p>\n<h3 class=\"subtitle\">Reference<\/h3>\n<p class=\"body\" align=\"justify\">H. Oshima, S. Re, Y. Sugita, Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules. <em>J Chem Theory Comput<\/em> 15, 5199-5208 (2019).<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Simulation Parameter Settings gamd YES \/ NO Default : NO Enable the GaMD method. boost YES \/ NO Default : YES Flag to apply GaMD boost to the system. If boost = NO, boost is not applied but GaMD parameters are updated from the trajectory. boost_type DUAL \/ DIHEDRAL \/ POTENTIAL Default: DUAL Type of &hellip; <a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/manual-of-gamd-in-genesis\/\" aria-label=\"Read more about GaMD-GENESIS: Manual\">Read more<\/a><\/p>\n","protected":false},"author":22429,"featured_media":0,"parent":2390,"menu_order":10,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2459","page","type-page","status-publish","hentry","odd"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.8 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>GaMD-GENESIS: Manual - Miao Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/manual-of-gamd-in-genesis\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"GaMD-GENESIS: Manual - Miao Lab\" \/>\n<meta property=\"og:description\" content=\"Simulation Parameter Settings gamd YES \/ NO Default : NO Enable the GaMD method. boost YES \/ NO Default : YES Flag to apply GaMD boost to the system. 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