{"id":144,"date":"2016-07-26T11:52:27","date_gmt":"2016-07-26T11:52:27","guid":{"rendered":"http:\/\/mech.sharif.ir\/~nejat\/?p=144"},"modified":"2019-02-03T06:34:05","modified_gmt":"2019-02-03T06:34:05","slug":"molecular-dynamics-2","status":"publish","type":"post","link":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/2016\/07\/26\/molecular-dynamics-2\/","title":{"rendered":"Molecular Dynamics"},"content":{"rendered":"<p><span style=\"font-size: 14pt;\"><strong>Syllabus:<\/strong><\/span><strong>\u00a0<\/strong><\/p>\n<ul>\n<li><strong>Introduction to the Application of the Molecular Dynamics for Modeling of the Nano-scale Systems <\/strong><\/li>\n<li><strong>Interatomic Potentials<\/strong><\/li>\n<li><strong>Energy Minimization and Related Methods for Exploring Energy Surfaces<\/strong><\/li>\n<li><strong>Computer Simulation Methods<\/strong><\/li>\n<li><strong>Molecular Dynamics Simulations Methods<\/strong><\/li>\n<li><strong>Introduction to Coarse Graining Methods<\/strong><\/li>\n<li><span style=\"color: #ff00ff;\"><strong>Monte Carlo Method<\/strong><\/span><\/li>\n<li><span style=\"color: #ff00ff;\"><strong>Statistical Mechanics<\/strong><\/span><\/li>\n<\/ul>\n<hr \/>\n<p><span style=\"font-size: 14pt;\"><strong>References:<\/strong><\/span><\/p>\n<ol>\n<li>A. R. Leach, Molecular Modelling: Principles and Applications, Prentice Hall, 2001.<\/li>\n<\/ol>\n<ol start=\"2\">\n<li>J. M. Haile, Molecular Dynamics Simulation: Elementary Methods, \u00a0Wiley-Interscience<\/li>\n<\/ol>\n<ol start=\"3\">\n<li>D. C. Rapaport , \u201cThe Art of Molecular Dynamics Simulation\u201d, Cambridge University Press, 2004.<\/li>\n<\/ol>\n<ol start=\"4\">\n<li>W. Humphrey, A. Dalke, and K. Schulten, \u201cVMD &#8211; Visual Molecular Dynamics\u201d, Journal of Molecular Graphics, vol. 14, p. 33-38, 1996.<\/li>\n<\/ol>\n<ol start=\"5\">\n<li>J. C. Phillips et al., \u201cScalable molecular dynamics with NAMD,\u201d Journal of computational chemistry, vol. 26, no. 16, p. 1781, 2005. \u201cNAMD A Parallel Object-Oriented Molecular Dynamics Program\u201d<\/li>\n<\/ol>\n<ol start=\"7\">\n<li>\u201cLAMMPS Molecular Dynamics Simulator\u201d. Sandia National Laboratories. Retrieved 2010-10-03.<\/li>\n<\/ol>\n<hr \/>\n<p><span style=\"font-size: 14pt;\"><strong>Slides:<\/strong><\/span><\/p>\n<p>Chapter 1:<\/p>\n<p>Chapter 2:<\/p>\n<hr \/>\n<p><span style=\"font-size: 14pt;\"><strong>Hws:<\/strong><\/span><\/p>\n<p>&nbsp;<\/p>\n<hr \/>\n<p><strong>Teaching\u00a0Assistant:\u00a0<span style=\"font-size: 14pt;\">Masoud Yousefi\u00a0<\/span>(masoud.yousefi71@gmail.com)<\/strong><\/p>\n<p dir=\"rtl\"><strong><span style=\"font-size: 14pt;\">\u0646\u06a9\u0627\u062a \u0645\u0647\u0645 \u062f\u0631 \u0627\u0631\u0633\u0627\u0644 \u062a\u0645\u0627\u0631\u06cc\u0646:<\/span><\/strong><br \/>\n\u0627\u062d\u062a\u0631\u0627\u0645\u0627 \u062a\u0642\u0627\u0636\u0627 \u0645\u06cc \u0634\u0648\u062f \u06a9\u0647 \u062f\u0627\u0646\u0634\u062c\u0648\u06cc\u0627\u0646 \u0645\u062d\u062a\u0631\u0645 \u062f\u0631\u0633 \u062f\u06cc\u0646\u0627\u0645\u06cc\u06a9 \u0645\u0648\u0644\u06a9\u0648\u0644\u06cc \u062c\u0647\u062a \u0627\u06cc\u0645\u06cc\u0644 \u062a\u06a9\u0627\u0644\u06cc\u0641 \u062e\u0648\u062f \u062f\u0631 \u0642\u0633\u0645\u062a \u0639\u0646\u0648\u0627\u0646 \u0627\u06cc\u0645\u06cc\u0644 \u0628\u0647 \u062a\u0631\u062a\u06cc\u0628 \u0645\u0648\u0627\u0631\u062f \u0632\u06cc\u0631 \u0631\u0627 \u062f\u0631\u062c \u0641\u0631\u0645\u0627\u06cc\u0646\u062f:<\/p>\n<div id=\"m_-1136093789863672710yui_3_16_0_1_1488189139748_11091\" dir=\"rtl\">MD_HW?_StudentName<\/div>\n<div id=\"m_-1136093789863672710yui_3_16_0_1_1488189139748_11091\" dir=\"rtl\">\u0628\u0627 \u062a\u0634\u06a9\u0631<\/div>\n<div id=\"m_-1136093789863672710yui_3_16_0_1_1488189139748_11091\" dir=\"rtl\">\u06cc\u0648\u0633\u0641\u06cc<\/div>\n<div dir=\"rtl\">\u0627\u06cc\u0645\u06cc\u0644:<strong>masoud.yousefi71@gmail.com<\/strong><\/div>\n<hr \/>\n<p>&nbsp;<\/p>\n<table width=\"533\">\n<tbody>\n<tr>\n<td width=\"64\"><\/td>\n<td width=\"124\">HW (100)<\/td>\n<td width=\"125\">Mid (120)<\/td>\n<td width=\"113\">Final(160)<\/td>\n<td width=\"107\">Total (20)<\/td>\n<\/tr>\n<tr>\n<td>94107894<\/td>\n<td>84.0<\/td>\n<td>89<\/td>\n<td>123<\/td>\n<td>17.4<\/td>\n<\/tr>\n<tr>\n<td>95201111<\/td>\n<td>94.0<\/td>\n<td>96<\/td>\n<td>138<\/td>\n<td>19.7<\/td>\n<\/tr>\n<tr>\n<td>95207471<\/td>\n<td>87.1<\/td>\n<td>77<\/td>\n<td>98<\/td>\n<td>16.6<\/td>\n<\/tr>\n<tr>\n<td>95209512<\/td>\n<td>20.5<\/td>\n<td>73<\/td>\n<td>96<\/td>\n<td>12<\/td>\n<\/tr>\n<tr>\n<td>96200485<\/td>\n<td>88.4<\/td>\n<td>79<\/td>\n<td>118<\/td>\n<td>17.2<\/td>\n<\/tr>\n<tr>\n<td>96207021<\/td>\n<td>83.3<\/td>\n<td>68<\/td>\n<td>100<\/td>\n<td>15.2<\/td>\n<\/tr>\n<tr>\n<td>96207098<\/td>\n<td>85.7<\/td>\n<td>102<\/td>\n<td>126<\/td>\n<td>18.7<\/td>\n<\/tr>\n<tr>\n<td>96208507<\/td>\n<td>86.0<\/td>\n<td>64<\/td>\n<td>108<\/td>\n<td>15.8<\/td>\n<\/tr>\n<tr>\n<td>96300274<\/td>\n<td>89.1<\/td>\n<td>75<\/td>\n<td>101<\/td>\n<td>16.8<\/td>\n<\/tr>\n<tr>\n<td>96302123<\/td>\n<td>96.0<\/td>\n<td>97<\/td>\n<td>142<\/td>\n<td>20<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"<p>Syllabus:\u00a0 Introduction to the Application of the Molecular Dynamics for Modeling of the Nano-scale Systems Interatomic Potentials Energy Minimization and Related Methods for Exploring Energy Surfaces Computer Simulation Methods Molecular Dynamics Simulations Methods Introduction to Coarse Graining Methods Monte Carlo Method Statistical Mechanics References: A. R. Leach, Molecular Modelling: Principles and Applications, Prentice Hall, 2001.<a href=\"http:\/\/mech.sharif.edu\/~nejat\/index.php\/2016\/07\/26\/molecular-dynamics-2\/\">[&#8230;]<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[9],"tags":[],"_links":{"self":[{"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/posts\/144"}],"collection":[{"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/comments?post=144"}],"version-history":[{"count":17,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/posts\/144\/revisions"}],"predecessor-version":[{"id":800,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/posts\/144\/revisions\/800"}],"wp:attachment":[{"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/media?parent=144"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/categories?post=144"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/tags?post=144"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}