{"id":2434,"date":"2023-09-19T16:22:02","date_gmt":"2023-09-19T20:22:02","guid":{"rendered":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/?page_id=2434"},"modified":"2025-02-14T12:52:26","modified_gmt":"2025-02-14T17:52:26","slug":"installation_namd","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/installation_namd\/","title":{"rendered":"GaMD-NAMD: Installation"},"content":{"rendered":"<h2>GaMD in NAMD2.13+\u00a0 <strong><br \/>\n<\/strong><\/h2>\n<p class=\"body\">GaMD has been fully supported in NAMD2.13+. <a href=\"http:\/\/www.ks.uiuc.edu\/Research\/namd\/\">Download NAMD from this webpage<\/a><\/p>\n<h2 class=\"body\">GaMD patch for NAMD2.11 \/ NAMD2.12: <strong><br \/>\n<\/strong><\/h2>\n<p class=\"body\">You can click the following link for a<a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/amber-gamd-tutorial.zip\"> patch that adds temporary support to NAMD 2.11 \/ NAMD2.12<\/a>\u00a0(zip file)<\/p>\n<h3 class=\"body\"><strong>Installation<\/strong><\/h3>\n<p class=\"body\">1. Replace the four NAMD2.11 source code files with those from the directory &#8220;.\/src_namd2.11&#8221;: &#8220;Controller.h&#8221;, &#8220;Controller.C&#8221;, &#8220;SimParameters.h&#8221; and &#8220;SimParameters.C&#8221;<\/p>\n<p class=\"body\">2. Re-compile NAMD following the <a href=\"http:\/\/www.ks.uiuc.edu\/Research\/namd\/\">original instructions.<\/a><\/p>\n<p>Precompiled GaMD-NAMD:<\/p>\n<p class=\"body\"><strong>On XSEDE Comet:<br \/>\n<\/strong>\/home\/yin\/namd_gamd-comet\/namd_2.11-gamd\/Linux-x86_64-icc\/namd2<\/p>\n<p class=\"body\"><strong>On XSEDE Gordon:<br \/>\n<\/strong>\/home\/yin\/namd_gamd\/namd_2.11-gamd\/Linux-x86_64-icc\/namd2<\/p>\n<h3 class=\"body\"><strong>Reference<\/strong><\/h3>\n<p class=\"body\">Pang, Y.T.<sup>#<\/sup>, Y. Miao<sup>#,*<\/sup>, Y. Wang<strong><sup>*<\/sup><\/strong> and J. A. McCammon<strong><sup>*<\/sup><\/strong> (2017) <a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jctc.6b00931\">Gaussian accelerated molecular dynamics in NAMD,<\/a> <em>J Chemical Theory and Computation,<\/em> <strong>13<\/strong>(1): 9-19.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>GaMD in NAMD2.13+\u00a0 GaMD has been fully supported in NAMD2.13+. Download NAMD from this webpage GaMD patch for NAMD2.11 \/ NAMD2.12: You can click the following link for a patch that adds temporary support to NAMD 2.11 \/ NAMD2.12\u00a0(zip file) Installation 1. Replace the four NAMD2.11 source code files with those from the directory &#8220;.\/src_namd2.11&#8221;: &hellip; <a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/installation_namd\/\" aria-label=\"Read more about GaMD-NAMD: Installation\">Read more<\/a><\/p>\n","protected":false},"author":22429,"featured_media":0,"parent":2390,"menu_order":7,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2434","page","type-page","status-publish","hentry","odd"],"acf":[],"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2434","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=2434"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2434\/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=2434"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}