Packmol<\/a> creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.<\/p>\n The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.<\/p>\n The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy.<\/p>\n The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.<\/p>\n Version 18.169 is installed.<\/p>\n None: MIT license.<\/p>\n To access the software you must first load the modulefile:<\/p>\n NOTE we now recommend loading the module file within your batch scripts.<\/p>\n Packmol is not parallelised, you should only run serial jobs.<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n See the Packmol web site<\/a> for usage and examples.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers. The user must provide only the coordinates of one.. Read more »<\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"parent":33,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1935","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/1935","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=1935"}],"version-history":[{"count":5,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/1935\/revisions"}],"predecessor-version":[{"id":1941,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/1935\/revisions\/1941"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/33"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=1935"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
module load apps\/intel-17.0\/packmol\/18.169<\/pre>\n
Running the application<\/h2>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\nmodule load apps\/intel-17.0\/packmol\/18.169\r\n\r\npackmol < filename.inp<\/em>\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Further info<\/h2>\n