{"id":2489,"date":"2023-09-19T18:48:17","date_gmt":"2023-09-19T22:48:17","guid":{"rendered":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/?page_id=2489"},"modified":"2024-01-17T15:27:10","modified_gmt":"2024-01-17T20:27:10","slug":"tutorial-of-gamd-in-namd","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/tutorial-of-gamd-in-namd\/","title":{"rendered":"GaMD-NAMD: Tutorial"},"content":{"rendered":"<h2 class=\"body\" align=\"justify\">Template input files for running GaMD in NAMD<\/h2>\n<p class=\"body\" align=\"justify\"><span class=\"body\"> In case you are running GaMD simulation on a computer cluster that imposes wallclock limit for simulation jobs, you may divide your long simulation into multiple jobs, which could include for example job #1 for 2 ns conventional MD (cMD) and 50 ns GaMD equilibration, job #2 for starting GaMD production simulation with radomized atomic velocities, and job #3 for extending GaMD production simulation until the end:<\/span><\/p>\n<h3 class=\"body\">Job #1: cMD and GaMD equilibration<\/h3>\n<p class=\"body\">accelMD \u00a0 \u00a0 \u00a0 \u00a0 on<br \/>\naccelMDdual \u00a0 \u00a0 on<br \/>\naccelMDdihe \u00a0 \u00a0 on<br \/>\naccelMDG \u00a0 \u00a0 \u00a0 \u00a0on<br \/>\naccelMDGiE \u00a0 \u00a0 \u00a01<br \/>\naccelMDGRestart\u00a0 off<br \/>\naccelMDGStatWindow\u00a0 20000<br \/>\naccelMDGcMDSteps\u00a0 1000000<br \/>\naccelMDGEquiSteps\u00a0 \u00a025000000<br \/>\naccelMDGcMDPrepSteps\u00a0 \u00a0 \u00a0 200000<br \/>\naccelMDGEquiPrepSteps\u00a0 \u00a0 \u00a0 \u00a0200000<br \/>\naccelMDOutFreq \u00a0$dcdfreq<br \/>\naccelMDGsigma0P 6.0<br \/>\naccelMDGsigma0D 6.0<br \/>\naccelMDGRestartFile \u00a0 \u00a0 \u00a0 ${molname}-out.restart.gamd<\/p>\n<p class=\"body\">run 26000000<\/p>\n<h3>Job #2: GaMD production simulation<\/h3>\n<p class=\"body\">accelMD \u00a0 \u00a0 \u00a0 \u00a0 on<br \/>\naccelMDdual \u00a0 \u00a0 on<br \/>\naccelMDdihe \u00a0 \u00a0 on<br \/>\naccelMDG \u00a0 \u00a0 \u00a0 \u00a0on<br \/>\naccelMDGiE \u00a0 \u00a0 \u00a01<br \/>\naccelMDGRestart on<br \/>\naccelMDGStatWindow\u00a0 20000<br \/>\naccelMDGcMDSteps \u00a0 \u00a0 \u00a0 \u00a00<br \/>\naccelMDGEquiSteps \u00a0 \u00a0 \u00a0 0<br \/>\naccelMDGcMDPrepSteps \u00a0 \u00a00<br \/>\naccelMDGEquiPrepSteps \u00a0 0<br \/>\naccelMDOutFreq \u00a0$dcdfreq<br \/>\naccelMDGsigma0P 6.0<br \/>\naccelMDGsigma0D 6.0<br \/>\naccelMDGRestartFile \u00a0 \u00a0 ${molname}-out.restart.gamd<\/p>\n<p class=\"body\">reinitvels $temperature<br \/>\nrun 25000000<\/p>\n<h3 class=\"body\">Job #3: repeat running jobs using this input file until end of your GaMD production simulation<\/h3>\n<p class=\"body\">accelMD \u00a0 \u00a0 \u00a0 \u00a0 on<br \/>\naccelMDdual \u00a0 \u00a0 on<br \/>\naccelMDdihe \u00a0 \u00a0 on<br \/>\naccelMDG \u00a0 \u00a0 \u00a0 \u00a0on<br \/>\naccelMDGiE \u00a0 \u00a0 \u00a01<br \/>\naccelMDGRestart on<br \/>\naccelMDGStatWindow\u00a0 20000<br \/>\naccelMDGcMDSteps \u00a0 \u00a0 \u00a0 \u00a00<br \/>\naccelMDGEquiSteps \u00a0 \u00a0 \u00a0 0<br \/>\naccelMDGcMDPrepSteps \u00a0 \u00a00<br \/>\naccelMDGEquiPrepSteps \u00a0 0<br \/>\naccelMDOutFreq \u00a0$dcdfreq<br \/>\naccelMDGsigma0P 6.0<br \/>\naccelMDGsigma0D 6.0<br \/>\naccelMDGRestartFile \u00a0 \u00a0 ${molname}-out.restart.gamd<\/p>\n<p class=\"body\">run 25000000<\/p>\n<p class=\"body\">Note: You can also perform multiple independent GaMD simulations with randomized atomic velocities by repeating jobs #2 and #3.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Template input files for running GaMD in NAMD In case you are running GaMD simulation on a computer cluster that imposes wallclock limit for simulation jobs, you may divide your long simulation into multiple jobs, which could include for example job #1 for 2 ns conventional MD (cMD) and 50 ns GaMD equilibration, job #2 &hellip; <a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/tutorial-of-gamd-in-namd\/\" aria-label=\"Read more about GaMD-NAMD: Tutorial\">Read more<\/a><\/p>\n","protected":false},"author":22429,"featured_media":0,"parent":2390,"menu_order":9,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2489","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\/2489","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=2489"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2489\/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=2489"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}