{"id":112,"date":"2014-06-28T13:55:48","date_gmt":"2014-06-28T04:55:48","guid":{"rendered":"http:\/\/fock2.c.s.osakafu-u.ac.jp\/~asada\/?page_id=112"},"modified":"2021-03-18T15:10:50","modified_gmt":"2021-03-18T06:10:50","slug":"%e3%83%97%e3%83%ad%e3%82%b0%e3%83%a9%e3%83%a0%e9%96%8b%e7%99%ba","status":"publish","type":"page","link":"https:\/\/polakow.fluid.me.omu.ac.jp\/~asada\/?page_id=112","title":{"rendered":"\u9ebb\u7530"},"content":{"rendered":"<p><strong><span style=\"font-size: 14pt; color: #ff0000;\">Plamas top page<\/span><\/strong><\/p><p><span style=\"color: #0000ff;\">PLAMAS<\/span>: Program package for Protein, Liquid, Amorphous, and Molecular Assembly (QM\/MM molecular dynamics simulation program for large molecules)<\/p><p>&nbsp;<\/p><p><span style=\"color: #ff0000;\">Implemented<\/span>:<\/p><p>Energy calculations, Structure Optimizations (Steepest Decent, Conjugate Gradient, BFGS, L-BFGS, Fire, Quick min algorithm), Molecular dynamics simulations (Constant energy, Periodic boundary conditions, Ewald method, Constant temperature: Nese-Hoover thermostat, Belly algorithm, Response Kernel Approximation), Electron (Hole) transfer integral: Marcus theory, Electron (Hole) mobility calculations, Free energy gradient, Nudged elastic band, Free energy reaction path optimization, Free energy contribution\u00a0analysis \u00a0 \u00a0<\/p><p>&nbsp;<\/p><p><span style=\"color: #ff0000;\">Reference of original techniques\u00a0used in this program.<\/span><\/p><p><span style=\"color: #0000ff;\">Charge and atom dipole response kernel approximation for QM(CDRK)\/MM method<\/span>. <span style=\"color: #000000;\">Efficient approach to include molecular polarizations using charge and atom dipole response kernels to calculate free energy gradients in QM\/MM scheme , Asada,K.Ando,K.Sakurai,S.Koseki,M.Nagaoka, <em>Phys.Chem.Chem.Phys.<\/em>,17, 26955 \u2013 26968 (2015).<\/span><\/p><p><span style=\"color: #000000;\"><span style=\"color: #0000ff;\">Free Energy Contribution Analysis<\/span> using Response Kernel Approximation: Insights into the Acylation Reaction for beta\u2013lactamase, T.Asada, K.Ando, P.Bandyopadhyay, S.Koseki,<em> J.Phys.Chem.B<\/em>, 120, 9338-9346 (2016).<\/span><\/p><p><span style=\"color: #0000ff;\">Hole\u00a0transfer integral calculations and hole mobility in the amorphous phase<\/span>. <span style=\"color: #000000;\">Amorphous Solid Simulation and Trial Fabrication of the Organic Field-Effect Transistor of Tetrathienonaphthalenes Prepared by Using Microflow Photochemical Reactions; A Theoretical Calculation-Inspired Investigation, Yamamoto, Atsushi; Matsui, Yasunori; Asada, Toshio; Kumeda, Motoki; Takagi, Kenichiro; Suenaga, Yu; Nagae, Kunihiko; Ohta, Eisuke; Sato, Hiroyasu; Koseki, Shiro; Naito, Hiroyoshi; Ikeda, Hiroshi, <em>J.Org.Chem.<\/em>,81, 3168-3176 (2016).<\/span> \u00a0<\/p><p><span style=\"color: #0000ff;\">Simulation study of hole mobility in the amorphous phase of organic molecules.<br \/><\/span>T. Asada and S.Koseki, Org.Elec., 53, 141-150 (2018)<\/p><p>Contact to: asada@c.s.osakafu-u.ac.jp<\/p>","protected":false},"excerpt":{"rendered":"<p>Plamas top pagePLAMAS: Program package for Protein, Liquid, Amorphous, and Molecular Assembly (QM\/MM molecular [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-112","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/polakow.fluid.me.omu.ac.jp\/~asada\/index.php?rest_route=\/wp\/v2\/pages\/112","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/polakow.fluid.me.omu.ac.jp\/~asada\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/polakow.fluid.me.omu.ac.jp\/~asada\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/polakow.fluid.me.omu.ac.jp\/~asada\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/polakow.fluid.me.omu.ac.jp\/~asada\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=112"}],"version-history":[{"count":13,"href":"https:\/\/polakow.fluid.me.omu.ac.jp\/~asada\/index.php?rest_route=\/wp\/v2\/pages\/112\/revisions"}],"predecessor-version":[{"id":1298,"href":"https:\/\/polakow.fluid.me.omu.ac.jp\/~asada\/index.php?rest_route=\/wp\/v2\/pages\/112\/revisions\/1298"}],"wp:attachment":[{"href":"https:\/\/polakow.fluid.me.omu.ac.jp\/~asada\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=112"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}