Parallel molecular dynamics code (home page<\/a>).<\/p>\n Two versions are available on CSF:<\/p>\n Due to license restrictions users must request access to the appropriate CSF Unix group, All users should read and follow the license<\/a>, a copy of which can be found The NAMD 2.9 (binary install) modulefile is loaded using:<\/p>\n The NAMD 2.7 (compiled on CSF) modulefile has a number of prerequisites. Hence you should load the following, for use with non-InfiniBand (GigE) connected nodes:<\/p>\n In all verisons executable is named: Load the appropriate modulefiles as listed above. Then create a jobscript in the directory containing your input files<\/em>, for example:<\/p>\n Submit the job using<\/p>\n where jobscript<\/em> is the name of your jobscript above.<\/p>\n Overview Parallel molecular dynamics code (home page). Two versions are available on CSF: Version 2.7 is compiled from source on the CSF (very limited access). Version 2.9 is a binary install. Restrictions on use Due to license restrictions users must request access to the appropriate CSF Unix group, namd or namdbin. Most users can only be granted access to the binary version. Please email its-ri-team@manchester.ac.uk for access. All users should read and follow the license,.. Read more »<\/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-320","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/320","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=320"}],"version-history":[{"count":17,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/320\/revisions"}],"predecessor-version":[{"id":4039,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/320\/revisions\/4039"}],"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=320"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}\n
Restrictions on use<\/h2>\n
namd<\/code> or namdbin<\/code>. Most users can only be granted access to the binary version. Please email its-ri-team@manchester.ac.uk<\/a> for access.<\/p>\n$NAMD_HOME\/license.txt<\/code>, but only once you have access to the module. The following points are of particular note:<\/p>\n\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/binapps\/namd\/2.9\r\n<\/pre>\n
\r\nmodule load compilers\/intel\/fortran\/11.1.064\r\nmodule load libs\/intel\/mkl\/10.2u3\r\nmodule load mpi\/intel-11.1\/openmpi\/1.4.3\r\nmodule load apps\/intel-11.1\/namd\/2.7\r\n<\/pre>\n
namd2<\/code><\/p>\nRequirements<\/h2>\n
\n
Example<\/h2>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd\r\n#$ -V\r\n#$ -pe smp.pe 8 # Example: 8 cores in this parallel environment (max 12)\r\n\r\n# NSLOTS is automatically set to the number of cores specified on the PE line\r\n\r\nmpirun -n $NSLOTS namd2\r\n<\/pre>\n
\r\nqsub jobscript<\/em>\r\n<\/pre>\n
Further info<\/h2>\n
\n