{"id":1975,"date":"2010-10-05T10:45:32","date_gmt":"2010-10-05T08:45:32","guid":{"rendered":"http:\/\/www.ehu.es\/sgi\/Arina\/?p=1975"},"modified":"2015-11-24T13:52:52","modified_gmt":"2015-11-24T11:52:52","slug":"amber-2","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/kalkulu-softwarea\/amber-2","title":{"rendered":"AMBER"},"content":{"rendered":"<h2>Informazio orokorra<\/h2>\n<p>AMBER (<strong>A<\/strong>ssisted\u00a0<strong>M<\/strong>odel\u00a0<strong>B<\/strong>uilding with\u00a0<strong>E<\/strong>nergy\u00a0<strong>R<\/strong>efinement) programaren 14. bertsioa eta AMBER-tools15. Potentzial enpirikoak erabiltzen dituen programa da eta dimanika molekularra eta energi minimizazioak egiten ditu. Sistema biologikoetarako erabiltzen da bereziki.<\/p>\n<h2>Nola erabili<\/h2>\n<p>Seriean eta paraleloan konpilatuta dago eta direktorio honetan topatu daitezke programak:<\/p>\n<pre>\/software\/bin\/amber\/<\/pre>\n<h3>send_amber<\/h3>\n<p>lanak kolara bidalteko <code>send_amber<\/code> tresna prestatu dugu:<\/p>\n<pre>send_amber \"Sander_options\" Nodes Procs_Per_Node[property] Time [or Queue] [Mem] [\"Other_queue_options\"]\r\n\r\n<strong>Sander_options<\/strong>: the options you want to use in the calculation, inside quotes\r\n<strong>Nodes<\/strong>: is the number of nodes\r\n<strong>Procs<\/strong>: is the number of processors (you may uinclude the node type) per node.\r\n<strong>Time<\/strong>: or Queue the walltime (in hh:mm:ss format) or the queue name of the calculation\r\n<strong>Mem<\/strong>: the PBS memory (in gb)\r\n[Mem] and [\"Other_queue_options\"] are optional<\/pre>\n<p>\u00abOther queue options\u00bb aukerarentzako see examples below:<\/p>\n<pre>send_amber \"sander.MPI -O -i in.md -c crd.md.23 -o file.out\" job1 1 8 p_slow\r\nsend_amber \"sander.MPI -O -i in.md -c crd.md.23 -o file.out\" 2 8:xeon vfast 16 \"-W depend=afterany:1234\"\r\nsend_amber \"sander.MPI -O -i in.md -c crd.md.23 -o file.out\" 4 8 24:00:00 32 \"-m be -M mi.email@ehu.es\"<\/pre>\n<h2>Informazio gehiago<\/h2>\n<p><a href=\"http:\/\/ambermd.org\/\" target=\"_blank\">Amber home page<\/a>.<\/p>\n<p><a href=\"http:\/\/ambermd.org\/doc12\/\" target=\"_blank\">On-line eskuliburua.<\/a><\/p>\n<p><a href=\"http:\/\/ambermd.org\/tutorials\/\" target=\"_blank\">Tutorialak<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Informazio orokorra AMBER (Assisted\u00a0Model\u00a0Building with\u00a0Energy\u00a0Refinement) programaren 14. bertsioa eta AMBER-tools15. Potentzial enpirikoak erabiltzen dituen programa da eta dimanika molekularra eta energi minimizazioak egiten ditu. Sistema biologikoetarako erabiltzen da bereziki. Nola erabili Seriean eta paraleloan konpilatuta dago eta direktorio honetan topatu daitezke programak: \/software\/bin\/amber\/ send_amber lanak kolara bidalteko send_amber tresna prestatu dugu: send_amber \u00abSander_options\u00bb Nodes Procs_Per_Node[property] &hellip; <a href=\"https:\/\/www.ehu.eus\/sgi\/kalkulu-softwarea\/amber-2\" class=\"more-link\">Seguir leyendo <span class=\"screen-reader-text\">AMBER<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_links_to":"","_links_to_target":""},"categories":[66],"tags":[],"_links":{"self":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/1975"}],"collection":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/comments?post=1975"}],"version-history":[{"count":7,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/1975\/revisions"}],"predecessor-version":[{"id":8289,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/1975\/revisions\/8289"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=1975"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=1975"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=1975"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}