From chemistry-request@www.ccl.net Mon Nov 2 13:42:12 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA00573 Mon, 2 Nov 1998 13:42:11 -0500 (EST) Received: from Amnesix.UQSS.UQuebec.ca (Amnesix.UQSS.UQuebec.CA [192.77.51.5]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id NAA10776 for ; Mon, 2 Nov 1998 13:42:06 -0500 (EST) From: jianhui_wu@IAF.UQUEBEC.CA Received: from poste.iaf.uquebec.ca by Amnesix.UQSS.UQuebec.ca with SMTP (1.37.109.24/15.6) id AA081362126; Mon, 2 Nov 1998 13:42:06 -0500 Received: from ccMail by poste.iaf.uquebec.ca (ccMail Link to SMTP R8.10.00) id AA910032257; Mon, 02 Nov 98 13:44:19 -0500 Message-Id: <9811029100.AA910032257@poste.iaf.uquebec.ca> X-Mailer: ccMail Link to SMTP R8.10.00 Date: Mon, 02 Nov 98 13:47:44 -0500 To: Subject: Summary: Discover, water ``evaporates`` Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Description: "cc:Mail Note Part" 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 ******************************************************************************** ****************************** 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 ********************************************************************* EOF