Summary: Discover, water ``evaporates``



 Hi,
 A few days ago, I ask a question regarding water ``evaporates`` during MD using
 Discover.
 I would like to thank Dr. Fiona Case and Dr. Don Gregory for their help (their
 responses
 are pasted as follow). First of all, the water didn`t evaperates!  ``As the
 water molecules
  wander out of the cell, their images re-enter the opposite side of the cell``.
 Since the InsightII
 tracks the original molecules only, it would give you a visual effect that some
 waters went out
 of the box. Re-imaging is done with Explicit Image model, but it is not done
 with Minimum
 Image model.
 Thanks a lot,
 JianHui Wu
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 ******************************
 Hi Dr. Wu,
 You can find some helpful information on MSI's scientific support,
 FAQ web-site.
 First go to:
 http://www.msi.com/support/FAQ.html
 and select the InsightII Core area.
 There you will find a tutorial on creating your own solvent boxes,
 and within the "How to Equilibrate the box" portion of that tutorial,
 you'll find a discussion on how to treat the 'visual' effect of waters/images
 outside the box.
 Hope this helps!
 Don Gregory
 ***************************************************************
 Hello,
 The water didn't evaporate. Its just that the
 particular water molecules you are displaying on
 the screen (the ones that started in the central
 or parent cell of your simulation) diffused
 through the bulk material (through the images of
 the central cell that you are not displaying
 right now).
 If you don't want any diffusion to take place you
 could, ofcourse, run the simulation at a very
 low temperature - but then nothing else much would
 happen either :-)
 If you want to see all the atoms within the central
 cell there are options to display in this mode.
 The commands are a little different depending on
 which user interface you use to access Discover.
 If you are using Discover from the InsightII user
 interface you can use the Assembly/Cell_Display
 command to display a "packed cell". If you are using
 the Cerius2 user interface you can use change the
 display mode using the menus accessed from the
 Crystal-Builder menu card.
 Hope this helps
 Fiona Case
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 EOF