{"id":410,"date":"2013-04-26T13:55:36","date_gmt":"2013-04-26T13:55:36","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=410"},"modified":"2017-09-15T14:35:23","modified_gmt":"2017-09-15T14:35:23","slug":"vmd","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/vmd\/","title":{"rendered":"VMD"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.<\/p>\n<p>Versions 1.8.7 and 1.9 are available. These are binary installs (i.e. no compilation involved).<\/p>\n<p>&nbsp;<\/p>\n<table style=\"text-align: center; width:66%; margin-left:22%; margin-right:22%;\">\n<tr>\n<td><em>Please do not run VMD directly on the login node. Such processes will be killed without warning.<\/em><\/td>\n<\/tr>\n<\/table>\n<p>&nbsp;<\/p>\n<h2>Restrictions on user access<\/h2>\n<p>There are no restrictions on accessing VMD, but all users should read and observe the <a href=\"http:\/\/www.ks.uiuc.edu\/Research\/vmd\/current\/LICENSE.html\">license<\/a>. In particular it should be noted that:<\/p>\n<ul>\n<li>VMD is for academic, research and internal business purposes only, e.g. not for commercial use. A definition of commercial use is given in clause 7.<\/li>\n<li>Citation of the software must appear in any published work. See clause 6 and <a href=\"http:\/\/www.ks.uiuc.edu\/Research\/vmd\/allversions\/cite.html\">the VMD website<\/a> for the required text.<\/li>\n<\/ul>\n<p>A copy of the license is also available on the CSF in: $VMD_HOME\/vmd\/LICENSE .<\/p>\n<h2>Set up procedure<\/h2>\n<p>You will need to connect to the CSF using <code>ssh -X<\/code> to have the display exported to your local machine. You should then load the appropriate VMD module using the <code>module<\/code> command to access the executables:<\/p>\n<ul>\n<li>For VMD 1.8.7: <code>module load apps\/binapps\/vmd\/1.8.7<\/code><\/li>\n<li>For VMD 1.9: <code>module load apps\/binapps\/vmd\/1.9<\/code><\/li>\n<\/ul>\n<p><a href=\"\/csf2\/getting-started-on-the-csf\/using-an-app-with-a-gui-x11-and-qrsh\/\">Further information about how to start X-Windows and GUI applications on the CSF<\/a>.<\/p>\n<h2>Running the application<\/h2>\n<p>The application is launched by issuing the command <code>vmd<\/code>.<\/p>\n<p>If you need to run the software for more than a few minutes using significant CPU or memory resources you should run it via a compute node thus:<\/p>\n<pre class=\"in1\">\r\nqrsh -V -l inter -l short vmd\r\n  #\r\n  # If you get an error about OpenGL see below\r\n<\/pre>\n<p>VMD will by default be restricted to a single CPU core. If you wish to run VMD multicore then you must override a VMD environment variable as follows:<\/p>\n<pre class=\"in1\">\r\n# Using 4 cores for example\r\nexport VMDFORCECPUCOUNT=4\r\nqrsh -V -l inter -l short -pe smp.pe $VMDFORCECPUCOUNT vmd\r\n  #\r\n  # If you get an error about OpenGL see below\r\n<\/pre>\n<h2>Exiting the Application<\/h2>\n<p>Please quit VMD (via the GUI) <em>before<\/em> you exit your ssh\/PuTTY login session on the CSF. If you simply quit your ssh application (e.g., kill PuTTY in Windows) then VMD is left running on the CSF.<\/p>\n<h2>Hints, Tips, Fixes<\/h2>\n<h3>Fix for OpenGL Error<\/h3>\n<p>You may get an error message from VMD about OpenGL such as:<\/p>\n<pre>\r\nERROR) A TrueColor visual is required, but not available.\r\nERROR) The X server is not capable of displaying double-buffered,\r\nERROR) RGB images with a Z buffer.   Exiting ...\r\nInfo) VMD for LINUXAMD64, version 1.9 (March 14, 2011)\r\nInfo) Unable to create OpenGL window.\r\n<\/pre>\n<p>Try setting the following variable before running qrsh \/ VMD:<\/p>\n<pre>\r\nexport LIBGL_ALWAYS_INDIRECT=1\r\n<\/pre>\n<div class=\"hidden\">\n<h3>Nvidia GPUs<\/h3>\n<p>VMD will make use of Nvidia CUDA hardware if present. This will accelerate raytraced rendering and implicit ligand sampling. If you have access to the GPU hardware (see <a href=\"\/csf-apps\/software\/applications\/nvidiagpu\">GPUs on the CSF<\/a>) you can run VMD as follows:<\/p>\n<pre class=\"in1\">\r\nunset VMDFORCECPUCOUNT\r\nqrsh -V -l inter -l nvidia vmd\r\n<\/pre>\n<\/div>\n<p>Please also consult the <a href=\"\/csf2\/csf-user-documentation\/sge-interactive-jobs-qrsh\">qrsh<\/a> documentation for more detailed instructions.<\/p>\n<h2>Further info<\/h2>\n<p>The <a href=\"http:\/\/www.ks.uiuc.edu\/Research\/vmd\/\">VMD website<\/a> has User Guides, Release Notes, and FAQs.<\/p>\n<h2>Updates<\/h2>\n<p>May &#8211; 2013 &#8211; Updated docs re OpenGL error fix<\/p>\n<p>March 2013 &#8211; Updated docs re multicore and GPUs.<\/p>\n<p>April 2011 &#8211; Version 1.9 installed.<\/p>\n<p>March 2011 &#8211; Version 1.8.7 installed.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Versions 1.8.7 and 1.9 are available. These are binary installs (i.e. no compilation involved). &nbsp; Please do not run VMD directly on the login node. Such processes will be killed without warning. &nbsp; Restrictions on user access There are no restrictions on accessing VMD, but all users should read and observe the license. In.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/vmd\/\">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-410","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/410","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=410"}],"version-history":[{"count":17,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/410\/revisions"}],"predecessor-version":[{"id":4265,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/410\/revisions\/4265"}],"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=410"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}