{"id":966,"date":"2018-11-22T16:29:12","date_gmt":"2018-11-22T16:29:12","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=966"},"modified":"2025-09-10T10:19:54","modified_gmt":"2025-09-10T09:19:54","slug":"charmm","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/charmm\/","title":{"rendered":"CHARMM"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>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<p>Version c36b2 of CHARMM is available, compiled with the xxlarge, MPI, COLFFT, MKL, PIPF, and DOMDEC options using Intel compilers v17.0.7.<\/p>\n<p>Version 46b2 of CHARMM is available, compiled with the MPI, FFTW3, MKL, COLFFT, Gaussin09 support and options using Intel compilers v19.1.2.<\/p>\n<h2>Restrictions on use<\/h2>\n<p><strong>charmm c36b2<\/strong> &#8211; this version is limited to one research group. The T&amp;C are very similar to those for 46b2.<\/p>\n<p><strong>charrmm 46b2<\/strong> may be used by UoM Staff and Students.<\/p>\n<p>Visitors\/Collaborators, even if they have a UoM IT username, are not permitted to access the software without the written consent of the CHARMM development project.<\/p>\n<p>All users who wish to access this software must read and agree to the <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-content\/uploads\/Charmm-free-academic-license-accessed-11thfeb2022-1630.pdf\">license<\/a>\u00a0 and confirm this to us via our <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/hpc-help\">help form<\/a>.<\/p>\n<p><strong>A summary of some important points from the license:<\/strong><\/p>\n<ul>\n<li>The software can only be used for internal non-commercial purposes which is defined in the license as:<\/li>\n<\/ul>\n<blockquote><p>\u201cacademic or other not-for-profit scholarly research which (a) is not undertaken for profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged in the commercial use, application or exploitation of works similar to CHARMM, unless such funding confers no commercial rights to the funding person or entity.\u201d<\/p><\/blockquote>\n<ul>\n<li>There is no access to the source code on the CSF<\/li>\n<li>You must cite your use of the software as per clause 11 of the license.<\/li>\n<li>Visitors\/Collaborators, even if they have a UoM IT username, are not permitted to access the software without the written consent of the CHARMM development project.<\/li>\n<\/ul>\n<h2>Set up procedure<\/h2>\n<p>To use CHARMM load the following modulefile:<\/p>\n<pre>\r\nmodule load apps\/intel-19.1\/charmm\/46b2\r\nmodule load apps\/intel-17.0\/charmm\/c36b2\r\n<\/pre>\n<p>The above modulefile will automatically load the appropriate compiler and MPI modulefiles.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run CHARMM on the login node. You must submit all work to batch.<\/p>\n<h3>Charmm 46b2<\/h3>\n<p>Charmm will\u00a0by default read a file named <code>charmm.inp<\/code> in the current directory if no input files are specified on the charmm command-line in your jobscript.<\/p>\n<p>Alternatively you may specify input and output files using command-line flags:<\/p>\n<pre>\r\ncharmm -i myinputfile.inp -o myoutputfile.out\r\n<\/pre>\n<p>A third method will <strong>fail<\/strong> when running in parallel where input\/output is done by reading from <em>stdin<\/em> and writing to <em>stdout<\/em> using a command-line such as:<\/p>\n<pre># This will FAIL when running charmm in parallel\r\ncharmm &lt; myinputfile.inp &gt; myoutputfile.out\r\n<\/pre>\n<p>It is safest to always use the <code>-i<\/code> and <code>-o<\/code> flags.<\/p>\n<h2>Serial job<\/h2>\n<p>An example batch submission script:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#SBATCH -p serial       # (or --partition=) Use the nodes dedicated to 1-core jobs\r\n#SBATCH -t 4-0          # 4 day wallclock (max permitted is 7 days)\r\n\r\nmodule purge\r\nmodule load apps\/intel-19.1\/charmm\/46b2\r\n\r\ncharmm\r\n<\/pre>\n<p>Submit with the command: <code>qsub <em>scriptname<\/em><\/code> where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2>Parallel job<\/h2>\n<h3>Single node job &#8211; 2 to 168 cores<\/h3>\n<p>An example batch submission script that will read a file named <code>charmm.inp<\/code> in the current directory:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#SBATCH -p multicore    # (or --partition=) Use the AMD 168-core jobs\r\n#SBATCH -n 16           # (or --ntasks=) Number of cores\r\n#SBATCH -t 4-0          # 4 day wallclock (max permitted is 7 days)\r\n\r\nmodule purge\r\nmodule load apps\/intel-19.1\/charmm\/46b2\r\n\r\nmpirun -n $SLURM_NTASKS charmm -i <em>myinputfile<\/em>.inp -o <em>myoutputfile<\/em>.out\r\n<\/pre>\n<p>Submit with the command <code>qsub <em>scriptname<\/em><\/code> where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<p>If your jobscript contains file input\/output using <em>redirection<\/em>, such as:<\/p>\n<pre>\r\n# WARNING: This will FAIL!\r\nmpirun -n $SLURM_NTASKS charmm &lt; myinputfile.inp &gt; myoutputfile.out\r\n<\/pre>\n<p>it will fail when run in parallel. Use the <code>-i<\/code> and <code>-o<\/code> flags instead.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/www.charmm.org\/\">CHARMM web pages<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None at this time.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>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 c36b2 of CHARMM is available, compiled with the xxlarge, MPI, COLFFT, MKL, PIPF, and DOMDEC options using Intel compilers v17.0.7. Version 46b2 of CHARMM is available, compiled with the MPI, FFTW3, MKL, COLFFT, Gaussin09 support and options using Intel compilers v19.1.2. Restrictions on use charmm c36b2 &#8211; this.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/charmm\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":8,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-966","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/966","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\/8"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=966"}],"version-history":[{"count":20,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/966\/revisions"}],"predecessor-version":[{"id":10921,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/966\/revisions\/10921"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=966"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}