{"id":3575,"date":"2017-02-08T11:31:53","date_gmt":"2017-02-08T11:31:53","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=3575"},"modified":"2018-12-03T15:15:10","modified_gmt":"2018-12-03T15:15:10","slug":"amber-dftb","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/amber\/amber-dftb\/","title":{"rendered":"DFTB Slater-Koster files usage in AMBER"},"content":{"rendered":"

Restrictions on use<\/h2>\n

As of February 2017 these files are available under a Creative Commons Attribution-ShareAlike License<\/a>. All users are therefor able to access and use them.<\/p>\n

Set up procedure<\/h2>\n

AMBER16<\/h3>\n

The files are available in AMBER16 in the $AMBERHOME\/dat\/slko<\/code> directory.<\/p>\n<\/h3>\n

AMBER12 or 14<\/h3>\n

Please do all of these steps in the directory from which you wish to submit your job.<\/p>\n

    \n
  1. Load the modulefile for the version of amber you wish to use. For example:\n
    \r\nmodule load apps\/intel-12.0\/amber\/14\r\n<\/pre>\n<\/li>\n
  2. Create a symlink to the central executable directory:\n
    \r\nln -s $AMBERHOME\/exe exe\r\n<\/pre>\n<\/li>\n
  3. Next we change the location of AMBERHOME<\/code> so that it points to where we have installed the Slater-Koster files relevant to your job. Importantly because we’ve already loaded the modulefile other essential things, such as intel compilers and mpi, remain unaffected by this
    \nvariable change:<\/p>\n
    \r\nexport AMBERHOME=$AMBERHOME\/dat\/slko\/3ob-3-1\r\n<\/pre>\n<\/li>\n
  4. Create a job submission script as usual and submit as usual.<\/li>\n<\/ol>\n
    Available files<\/h2>\n
    All – Amber16 – available by default in $AMBERHOME\/dat\/slko
    \nmio-1-1 – installed 13 Feb 2017 (Amber12 and 14).
    \n3ob-3-1 – installed 09 Dec 2016 (Amber 12 and 14).<\/p>\n
    Other sets can be installed in request providing the Restrictions on Use are met.<\/p>\n","protected":false},"excerpt":{"rendered":"
    Restrictions on use As of February 2017 these files are available under a Creative Commons Attribution-ShareAlike License. All users are therefor able to access and use them. Set up procedure AMBER16 The files are available in AMBER16 in the $AMBERHOME\/dat\/slko directory. AMBER12 or 14 Please do all of these steps in the directory from which you wish to submit your job. Load the modulefile for the version of amber you wish to use. For example:.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":731,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-3575","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/3575","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=3575"}],"version-history":[{"count":20,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/3575\/revisions"}],"predecessor-version":[{"id":4965,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/3575\/revisions\/4965"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/731"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=3575"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}