{"id":98,"date":"2018-11-29T12:52:38","date_gmt":"2018-11-29T17:52:38","guid":{"rendered":"http:\/\/fakemembrane.urmc.rochester.edu\/wordpress\/?page_id=98"},"modified":"2019-04-26T10:38:30","modified_gmt":"2019-04-26T14:38:30","slug":"running-smog-simulations-in-openmm","status":"publish","type":"page","link":"http:\/\/membrane.urmc.rochester.edu\/?page_id=98","title":{"rendered":"Using SMOG models in OpenMM"},"content":{"rendered":"<p>Our group has recently added support for running SMOG models in OpenMM. &nbsp;OpenMM is a modern Molecular Dynamics package that includes full GPU support out of the box and is easy to customize. &nbsp;In order to use SMOG models in OpenMM, we recommend the following steps:<\/p>\n<ol>\n<li>Get OpenMM from Conda.<\/li>\n<li>Submit your PDB file to&nbsp;the <a href=\"http:\/\/smog-server.org\/cgi-bin\/GenTopGro.pl\">SMOG web server<\/a> and get the GROMACS input files.&nbsp;Currently only the all-atom model is supported in OpenMM. Note that use of the SMOG web server is not required as the SMOG2 standalone software also supports the all-atom model. Alternatively, you can download the SMOG example model that is found <a href=\"http:\/\/smog-server.org\/2ci2.smog.tar.gz\">here<\/a>.<\/li>\n<li>Download our <a href=\"http:\/\/membrane.urmc.rochester.edu\/sites\/default\/files\/dynamics.py\">dynamics.py<\/a> script and call it using the SMOG&nbsp;.gro and .top files as inputs:<br \/>\n<code>.\/dynamics.py your.gro your.top your.dcd<\/code><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>Our group has recently added support for running SMOG models in OpenMM. &nbsp;OpenMM is a modern Molecular Dynamics package that includes full GPU support out of the box and is easy to customize. &nbsp;In order to use SMOG models in OpenMM, we recommend the following steps: Get OpenMM from Conda. Submit your PDB file to&nbsp;the &hellip; <\/p>\n<p class=\"link-more\"><a href=\"http:\/\/membrane.urmc.rochester.edu\/?page_id=98\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Using SMOG models in OpenMM&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-98","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/membrane.urmc.rochester.edu\/index.php?rest_route=\/wp\/v2\/pages\/98","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/membrane.urmc.rochester.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/membrane.urmc.rochester.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/membrane.urmc.rochester.edu\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/membrane.urmc.rochester.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=98"}],"version-history":[{"count":3,"href":"http:\/\/membrane.urmc.rochester.edu\/index.php?rest_route=\/wp\/v2\/pages\/98\/revisions"}],"predecessor-version":[{"id":523,"href":"http:\/\/membrane.urmc.rochester.edu\/index.php?rest_route=\/wp\/v2\/pages\/98\/revisions\/523"}],"wp:attachment":[{"href":"http:\/\/membrane.urmc.rochester.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=98"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}