{"id":2417,"date":"2023-09-19T15:30:40","date_gmt":"2023-09-19T19:30:40","guid":{"rendered":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/?page_id=2417"},"modified":"2023-10-11T18:15:31","modified_gmt":"2023-10-11T22:15:31","slug":"installation","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/installation\/","title":{"rendered":"GaMD-Amber: Installation"},"content":{"rendered":"<h2>LiGaMD in Amber20<\/h2>\n<p class=\"body\">LiGaMD has been fully supported in AMBER20, which was released in May 2020 and can be obtained at the <a href=\"http:\/\/ambermd.org\">Amber website<\/a>.\u00a0Instructions for installing the AMBER package can be found in the <a href=\"http:\/\/ambermd.org\/doc12\/Amber20.pdf\">AMBER manual<\/a>.<\/p>\n<h2>GaMD in Amber16+<\/h2>\n<p>GaMD has been fully supported in AMBER16+ since AMBER16 was released on Apr 30, 2016.<\/p>\n<h2>GaMD patch for Amber14<\/h2>\n<p class=\"body\">&#8220;amber14_GaMD_patch_confidential.txt&#8221;:<br \/>\nGaMD patch for Amber 14 + AmberTools 15<br \/>\nAuthors: Yinglong Miao &amp; Ross C. Walker<br \/>\nDate: 29th July 2015<br \/>\nPrograms: pmemd and pmemd.cuda<br \/>\nDescription: This patch adds temporary GaMD support to AMBER 14.<br \/>\nIt is built against AMBER 14 + AmberTools 15 + Amber 14 updates to 12.<br \/>\nThis patch is provided for convenience prior to AMBER 16 release which<br \/>\nwill feature GaMD support. It is made available by request only and subject<br \/>\nto your agreement not to redistribute this patch or to provide access to<br \/>\na GaMD patched copy of AMBER without the written permission of<br \/>\nRoss C. Walker or Yinglong Miao.<\/p>\n<p>By applying this patch you accept these terms and certify that you have<br \/>\nbeen granted permission to use this with Amber 14 + AmberTools 15.<\/p>\n<p>Suppose you have installed &#8220;AMBER 14 + AmberTools 15&#8221; (<a href=\"http:\/\/ambermd.org\" rel=\"noopener noreferrer\">Amber website<\/a>).<br \/>\nYou can apply the GaMD patch and compile the code as the following:<\/p>\n<p># Uncompress the patch<br \/>\ntar -xvzf amber14-gamd-patch.tgz<\/p>\n<p># Apply the GaMD patch<br \/>\n# export AMBERHOME to your amber home directory<br \/>\ncp -v amber14_GaMD_patch_confidential.txt $AMBERHOME<br \/>\ncd $AMBERHOME<br \/>\n.\/update_amber &#8211;update<br \/>\npatch -p0 &lt; amber14_GaMD_patch_confidential.txt<\/p>\n<p># Re-compile the AMBER code<br \/>\ncd $AMBERHOME<br \/>\n.\/configure gnu<br \/>\ncd $AMBERHOME\/src\/pmemd\/src<br \/>\nmake install<\/p>\n<p>cd $AMBERHOME<br \/>\n.\/configure -cuda gnu<br \/>\ncd $AMBERHOME\/src\/pmemd\/src<br \/>\nmake cuda<\/p>\n","protected":false},"excerpt":{"rendered":"<p>LiGaMD in Amber20 LiGaMD has been fully supported in AMBER20, which was released in May 2020 and can be obtained at the Amber website.\u00a0Instructions for installing the AMBER package can be found in the AMBER manual. GaMD in Amber16+ GaMD has been fully supported in AMBER16+ since AMBER16 was released on Apr 30, 2016. GaMD &hellip; <a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/installation\/\" aria-label=\"Read more about GaMD-Amber: Installation\">Read more<\/a><\/p>\n","protected":false},"author":22429,"featured_media":0,"parent":2390,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2417","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-Amber: Installation - 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\/installation\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"GaMD-Amber: Installation - Miao Lab\" \/>\n<meta property=\"og:description\" content=\"LiGaMD in Amber20 LiGaMD has been fully supported in AMBER20, which was released in May 2020 and can be obtained at the Amber website.\u00a0Instructions for installing the AMBER package can be found in the AMBER manual. GaMD in Amber16+ GaMD has been fully supported in AMBER16+ since AMBER16 was released on Apr 30, 2016. 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GaMD in Amber16+ GaMD has been fully supported in AMBER16+ since AMBER16 was released on Apr 30, 2016. GaMD &hellip; Read more","og_url":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/installation\/","og_site_name":"Miao Lab","article_modified_time":"2023-10-11T22:15:31+00:00","twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/installation\/","url":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/installation\/","name":"GaMD-Amber: Installation - Miao Lab","isPartOf":{"@id":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/#website"},"datePublished":"2023-09-19T19:30:40+00:00","dateModified":"2023-10-11T22:15:31+00:00","breadcrumb":{"@id":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/installation\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/installation\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/installation\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/"},{"@type":"ListItem","position":2,"name":"Resources","item":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/"},{"@type":"ListItem","position":3,"name":"GaMD","item":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/"},{"@type":"ListItem","position":4,"name":"GaMD-Amber: Installation"}]},{"@type":"WebSite","@id":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/#website","url":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/","name":"Miao Lab","description":"Department of Pharmacology","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"}]}},"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2417","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/users\/22429"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/comments?post=2417"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2417\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2390"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/media?parent=2417"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}