{"id":1155,"date":"2013-11-21T09:50:11","date_gmt":"2013-11-21T09:50:11","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=1155"},"modified":"2015-04-09T10:33:18","modified_gmt":"2015-04-09T10:33:18","slug":"towhee","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/towhee\/","title":{"rendered":"Towhee"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>Towhee is a Monte Carlo molecular simulation code.<\/p>\n<p>Version 7.0.6 is installed on the CSF and was compiled using Intel 12.0.5 compilers. The Utils were added in April 2015. <code>forcefield<\/code> binary is missing please use the newer version for that.<\/p>\n<p>Version 7.1.0 is also installed and was compiled using Intel 14.0.3 compilers and the optimisation flags -O3 and -axAVX were used. It includes all the Utils and the <code>forcefield<\/code> binary.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>All users may access Towhee. Please ensure you correctly cite your usage of this software as detailed in the <a href=\"http:\/\/towhee.sourceforge.net\/citation_manual.html\">Towhee Citation<\/a>.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile for the version you wish to use:<\/p>\n<pre>\r\nmodule load apps\/intel-14.0\/towhee\/7.1.0\r\n<\/pre>\n<pre>\r\nmodule load apps\/intel-12.0\/towhee\/7.0.6\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run Towhee on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded. <\/p>\n<p>Place all the input and other files required by your job into your working directory.<\/p>\n<p>Then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -cwd\r\n#$ -V\r\n\r\ntowhee\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub scriptname<\/pre>\n<h3>Parallel batch job submission<\/h3>\n<p>Towhee cannot run parallel jobs. It has not been compiled with mpi enabled because the software uses MPI only to spawn serial jobs. We strongly recommend the use of <a href=\"\/csf2\/csf-user-documentation\/sge-job-arrays\/\">SGE Job Arrays<\/a> for running multiple serial jobs.<\/p>\n<h2> Examples and ForceFields files<\/h2>\n<p>The install of Towhee has some examples and ForceFields files available. <\/p>\n<p>To use the examples, copy the one you are interested in to your scratch area, e.g.:<\/p>\n<pre>\r\ncd scratch\r\ncp -r $TOWHEE_HOME\/Examples\/Canonical_Ensemble\/AVB1_Methane .\r\n<\/pre>\n<p>Now change the ForceFields line in the <code>towhee_input<\/code> file. For example from:<\/p>\n<pre>\r\n\/towheebase\/ForceFields\/towhee_ff_Charmm27\r\n<\/pre>\n<p>to<\/p>\n<pre>\r\n\/opt\/gridware\/apps\/intel-12.0\/towhee\/7.0.6\/ForceFields\/towhee_ff_Charmm27\r\n<\/pre>\n<p>or<\/p>\n<pre>\r\n\/opt\/gridware\/apps\/intel-14.0\/towhee\/7.1.0\/ForceFields\/towhee_ff_Charmm27\r\n<\/pre>\n<p>You can also make use of the ForceFields files for your own jobs.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/towhee.sourceforge.net\/\">The Towhee website<\/a> has manuals, examples, and other reference material.<\/li>\n<li><a href=\"http:\/\/sourceforge.net\/p\/towhee\/discussion\/\">Towhee forum<\/a>.<\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>April 2015 &#8211; 7.1.0 installed and ensured Utils and <code>forcefield<\/code> binary were included.<br \/>\nApril 2015 &#8211; Utils added to 7.0.6.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Towhee is a Monte Carlo molecular simulation code. Version 7.0.6 is installed on the CSF and was compiled using Intel 12.0.5 compilers. The Utils were added in April 2015. forcefield binary is missing please use the newer version for that. Version 7.1.0 is also installed and was compiled using Intel 14.0.3 compilers and the optimisation flags -O3 and -axAVX were used. It includes all the Utils and the forcefield binary. Restrictions on use All.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/towhee\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1155","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1155","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=1155"}],"version-history":[{"count":20,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1155\/revisions"}],"predecessor-version":[{"id":2388,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1155\/revisions\/2388"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=1155"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}