tag:blogger.com,1999:blog-5744790168115177005.post3871632493798006515..comments2024-03-02T07:26:51.612+01:00Comments on Proteins and Wave Functions: Discussion of the Friesner PaperJan Jensenhttp://www.blogger.com/profile/08595894308946022740noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-5744790168115177005.post-7909689493922786472011-03-03T12:41:25.655+01:002011-03-03T12:41:25.655+01:00PS. You forgot to mention that the paper and slide...PS. You forgot to mention that the paper and slides can be found at https://sites.google.com/site/qmmmatku/week-4Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-64063197318583545662011-03-03T12:39:44.076+01:002011-03-03T12:39:44.076+01:00I assume the water was equilibrated with periodic ...I assume the water was equilibrated with periodic boundary conditions, so this water should be a snapshot of bulk water, and would change drastically if optimized in vacuum. So I think it is important for the outermost layer to be frozen.<br /><br />We also discussed this statement from the paper (pg 1423): "Water molecules beyond 10 Å from the protein were deleted and the oxygen atoms of water molecules 6-10 Å from the protein were frozen throughout the following calculation."<br /><br />It is not clear what "from the protein" means. Some point in the active site, or the protein surface. If the latter, how was it defined?Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.com