{"id":747,"date":"2015-12-15T16:03:42","date_gmt":"2015-12-15T21:03:42","guid":{"rendered":"https:\/\/bmcresearch.utm.utoronto.ca\/sciencevislab\/?p=747"},"modified":"2015-12-15T16:03:42","modified_gmt":"2015-12-15T21:03:42","slug":"simulating-molecular-water","status":"publish","type":"post","link":"https:\/\/sciencevis.ca\/index.php\/2015\/12\/15\/simulating-molecular-water\/","title":{"rendered":"Simulating molecular water"},"content":{"rendered":"[vc_row type=”in_container” scene_position=”center” text_color=”dark” text_align=”left”][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”2\/3″][vc_column_text]As part of one of the\u00a0Molecular Visualization Principles, I am attempting to\u00a0design a simulation of molecular water with correct scale, density, and an approximation of brownian motion.<\/p>\n

I began by\u00a0creating a very simple water molecule model, ensuring that the\u00a0dimensions were accurate. Okay, the bond angles might be very slightly out, but who would ever be able to tell? I knew there were going to be a\u00a0huge number of copies, so keeping the poly count low was a must.<\/p>\n

When making the simulation, I decided to ignore hydrogen bonding interactions, but I did use the bonding radius for\u00a0the collision radius, which created a natural looking separation between the molecules.<\/p>\n

In order to determine how the simulation would look once rendered, I made a\u00a0small cube’s worth of molecules at the\u00a0size, speed, and resolution I\u00a0would be using for the final animation. This is the reason it takes up only a small part of the frame. If the result was a fuzzy blurry mess, I would know that changes were required.<\/p>\n

A used a hand animated sphere as a collider and included noisy turbulence to induce brownian motion. The final animation will include a lateral wipe to show and hide the water, so I made sure to include a simple test of that.\u00a0The result is below, and I\u00a0think it is successful enough to move on to the full scale simulation.[\/vc_column_text][\/vc_column][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”1\/3″]

\"\"<\/div><\/div>[vc_column_text]Measured bond length: 0.9584\u00a0Angstroms<\/p>\n

Measured bond angle: 107.9 degrees[\/vc_column_text]

\"\"<\/div><\/div>[\/vc_column][\/vc_row][vc_row type=”in_container” scene_position=”center” text_color=”dark” text_align=”left”][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”1\/1″][vc_video link=”https:\/\/www.youtube.com\/watch?v=5F4JoMsD3OE”][\/vc_column][\/vc_row]\n","protected":false},"excerpt":{"rendered":"

[vc_row type=”in_container” scene_position=”center” text_color=”dark” text_align=”left”][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”2\/3″][vc_column_text]As part of one of the\u00a0Molecular Visualization Principles, I am attempting to\u00a0design a simulation of molecular water with correct scale, density,…<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,26],"tags":[],"class_list":{"0":"post-747","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-molecular","7":"category-process"},"_links":{"self":[{"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/posts\/747","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/comments?post=747"}],"version-history":[{"count":6,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/posts\/747\/revisions"}],"predecessor-version":[{"id":755,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/posts\/747\/revisions\/755"}],"wp:attachment":[{"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/media?parent=747"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/categories?post=747"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/tags?post=747"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}