CHARMM is a many-particle molecular simulation program which focuses on biological systems, e.g. peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates. <\/p>\n
Version c35b2 and c36b2 of CHARMM are available both compiled with the xlarge, MPI and em64t options using Intel compilers v11.1. Version c36b2 has also been compiled with the Intel 12.0 compiler (e.g., for use with ChemShell<\/a> 3.5.0 which has also been compiled with the Intel 12.0 compiler).<\/p>\n The CHARMM installs are restricted to specific research groups. Only these groups may use the software and only the version they have a license for. The head of any research group holding a license can email its-ri-team@manchester.ac.uk<\/a> to find out how to get access to CHARMM.<\/p>\n Version c35b2 – A full copy of the license is available from the Head of the Research Group.<\/p>\n Version c36b2 – A full copy of the license is available in Important points to note are:<\/p>\n Users wishing to access the software should request access via its-ri-team@manchester.ac.uk<\/a>. A confirmation email will be sent once a user has been added to the appropriate unix group and users who are not part of an eligible research group will be given additional advice on how to proceed.<\/p>\n To use CHARMM load one<\/em> of the following modulefiles: <\/p>\n The above modulefiles will automatically load the appropriate compiler and MPI modulefiles.<\/p>\n Charmm will read a file named Alternatively you may specify input and output files using command-line flags:<\/p>\n A third method will fail<\/strong> when running in parallel where input\/output is done by reading from stdin<\/em> and writing to stdout<\/em> using a command-line such as:<\/p>\n It is safest to always use the First load the required module (see above) and create a directory containing a file called charmm.inp containing the job parameters. <\/p>\n Note: a feature of the MPI, em64t c35b2 version of CHARMM is that it will read input only from a file named charmm.inp, i.e. CHARMM will not read from standard input. This is described here<\/a>. If you see messages which look like:<\/p>\n it is likely to be for this reason.<\/p>\n 1. An example batch submission script:<\/p>\n 2. Submit with the command: `qsub scriptname`<\/p>\n Ensure you have an modulefile without ‘ib’ in the name loaded.<\/p>\n An example batch submission script that will read a file named Submit with the command Ensure you have loaded a charmm modulefile with An example batch submission script that will read a file named Submit with the command The following is an example batch submission script that will read and write named files:<\/p>\n Submit the job using If your jobscript contains file input\/output using redirection, such as:<\/p>\n it will fail when run in parallel. Use the None at this time.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview CHARMM is a many-particle molecular simulation program which focuses on biological systems, e.g. peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates. Version c35b2 and c36b2 of CHARMM are available both compiled with the xlarge, MPI and em64t options using Intel compilers v11.1. Version c36b2 has also been compiled with the Intel 12.0 compiler (e.g., for use with ChemShell 3.5.0 which has also been compiled with the Intel 12.0 compiler). Restrictions.. 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-79","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/79","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=79"}],"version-history":[{"count":14,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/79\/revisions"}],"predecessor-version":[{"id":3243,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/79\/revisions\/3243"}],"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=79"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
\/opt\/gridware\/apps\/intel-11.1\/charmm\/c36b2\/CharmmLicenseForm.pdf<\/code><\/p>\n\n
Set up procedure<\/h2>\n
\r\n# Version c35b2\r\nmodule load apps\/intel-11.1\/charmm\/c35b2\r\n\r\n# Version c36b2 (with different compiler versions and possibly infiniband)\r\nmodule load apps\/intel-12.0\/charmm\/c36b2-ib # Use for multi-node MPI jobs\r\nmodule load apps\/intel-12.0\/charmm\/c36b2\r\nmodule load apps\/intel-11.1\/charmm\/c36b2\r\n<\/pre>\n
Running the application<\/h2>\n
Charmm c36b2<\/h3>\n
charmm.inp<\/code> in the current directory if no input files are specified on the charmm command-line in your jobscript (never run charmm on the login node!)<\/p>\n\r\ncharmm -i myinputfile.inp -o myoutputfile.out\r\n<\/pre>\n
\r\n# This will FAIL when running charmm in parallel\r\ncharmm < myinputfile.inp > myoutputfile.out\r\n<\/pre>\n
-i<\/code> and -o<\/code> flags.<\/p>\nCharmm c35b2<\/h3>\n
\r\n# forrtl: No such file or directory\r\n# forrtl: severe (29): file not found, unit 5, file \/opt\/gridware\/apps\/intel-11.1\/charmm\/c35b2\/test\/charmm.inp\r\n<\/pre>\n
Serial job<\/h2>\n
\r\n### SGE Job Stuff\r\n#$ -cwd\r\n#$ -V\r\n\r\ncharmm\r\n<\/pre>\n
Parallel job<\/h2>\n
Single node job – 2 to 24 cores<\/h3>\n
charmm.inp<\/code> in the current directory:<\/p>\n\r\n#!\/bin\/bash\r\n#$ -S bash\r\n#$ -cwd\r\n#$ -V\r\n#$ -pe smp.pe 8 # Use 8 cores on a single node. Min 2, max 24.\r\n\r\nmpiexec -n $NSLOTS charmm\r\n<\/pre>\n
qsub scriptname<\/em><\/code> where scriptname<\/em> is the name of your jobscript from above.<\/p>\nMulti-node jobs – 48+ cores<\/h3>\n
-ib<\/code> in the name.<\/p>\ncharmm.inp<\/code> in the current directory:<\/p>\n\r\n#!\/bin\/bash\r\n#$ -S bash\r\n#$ -cwd\r\n#$ -V\r\n#$ -pe orte-24-ib 48 # Use two nodes, each with 24 cores\r\n\r\nmpiexec -n $NSLOTS charmm\r\n<\/pre>\n
qsub scriptname<\/em><\/code> where scriptname<\/em> is the name of your jobscript from above.<\/p>\n\r\n#!\/bin\/bash\r\n#$ -S bash\r\n#$ -cwd\r\n#$ -V\r\n#$ -pe orte-24-ib 48 # Use two nodes, each with 24 cores\r\n\r\nmpiexec -n $NSLOTS charmm -i myinputfile.inp -o myoutputfile.out\r\n<\/pre>\n
qsub jobscript<\/em><\/code> where jobscript<\/em> is the name of your script above.<\/p>\n\r\n# WARNING: This will FAIL!\r\nmpiexec -n $NSLOTS charmm < myinputfile.inp > myoutputfile.out\r\n<\/pre>\n
-i<\/code> and -o<\/code> flags instead.<\/p>\nFurther info<\/h2>\n
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Updates<\/h2>\n