Subject: Summary: Discover, water ``evaporates``

From: [email-masked]
Date: Mon, 02 Nov 98 13:47:44 -0500

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
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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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