From chemistry-request@ccl.net Sat Oct 9 09:06:57 2004 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i99E6uWJ019223 for ; Sat, 9 Oct 2004 09:06:57 -0500 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.14) id 1CGI3G-0007gA-Io for chemistry|at|ccl.net; Sat, 09 Oct 2004 15:18:26 +0100 Received: from mmm1.mats.qmul.ac.uk ([138.37.43.102] helo=mmm1) by smtp.qmul.ac.uk with smtp (Exim 4.34) id 1CGI3G-0005LK-14 for chemistry|at|ccl.net; Sat, 09 Oct 2004 15:18:26 +0100 Message-ID: <001e01c4ae0c$2543afd0$662b258a@mmm1> From: "Ru-Zhen Li" To: Subject: molecules came out of MD cell Date: Sat, 9 Oct 2004 15:27:46 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001B_01C4AE14.86FE7AE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Sender-Host-Address: 138.37.43.102 X-QM-Scan-Virus: virusscan says the message is clean X-QM-Scan-Virus: ClamAV says the message is clean X-Spam-Status: No, hits=4.0 required=7.5 tests=HTML_30_40,HTML_MESSAGE, NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_001B_01C4AE14.86FE7AE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, I am doing a MD simulation, and found out that some molecules came out = of the simulating cell, as I used PBC, it makes sense in the beginning = that while some atoms came out of the cell, there should be the same = atoms got into this cell, however, if this is the case, there should be = a net flow of mass in the whole system, then how MD will handle this? = because as far as I know in first principle, this is not allowed. can any one give me some ideas how to explain this? Thanks a lot, Best Regards, RZ ------=_NextPart_000_001B_01C4AE14.86FE7AE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
 
I am doing a MD simulation, and found = out that some=20 molecules came out of the simulating cell, as I used PBC, it makes sense = in the=20 beginning that while some atoms came out of the cell, there should be = the same=20 atoms got into this cell, however, if this is the case, there should be = a net=20 flow of mass in the whole system, then how MD will handle this? = because as=20 far as I know in first principle, this is not allowed.
 
can any one give me some ideas how to = explain=20 this?
 
Thanks a lot,
 
Best Regards,
 
RZ 
------=_NextPart_000_001B_01C4AE14.86FE7AE0-- From chemistry-request@ccl.net Sat Oct 9 17:11:18 2004 Received: from mail.interware.hu (mail.interware.hu [195.70.32.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i99MBGps023110 for ; Sat, 9 Oct 2004 17:11:16 -0500 Received: from caracas-1129.adsl.interware.hu ([213.178.104.105] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.34 #1 (Debian)) id 1CGPbz-00062B-Qp; Sun, 10 Oct 2004 00:22:48 +0200 Message-ID: <009101c4ae57$59716d10$0200a8c0@cthulhu> From: "Tamas E. Gunda" To: "Joe Patrick" , References: <4165884A.8060403_at_hyper.com> Subject: Re: CCL:HyperChem Date: Sun, 10 Oct 2004 00:26:04 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Mr Patrick, I use HyperChem since version 3 (currently 7.1). generally speaking, I like Hyperchem and it can be used very good in teaching, although quite expensive. Sometimes it's argued that it is slow. I do not want to say any pros or contras because I did not make any serious comparisons with other program applications using the same hardware. However, there are several issues which could already have been solved long ago: 1) Its interface would need a face-lift. I do understand that programmers are reluctant to touch already finished and seemingly permanent modules, however, there are some options/functions which would greatly help the user-friendliness of the program, for example: a) Last opened files in the File menu - should have been implanted several versions ago. b) Undo - very needed when editing a molecule and accidental changes should be reversed. I do know that it is not at all easy to implant into a ready program, however a simple one-step undo would be also of great help. c) Rotation/Translation/Zoom modes are available only by the toolbar buttons. Most other applications use the shift/ctrl/alt + mouse-drag combinations, which are more flexible and quicker to use. 2) Initialization of File open/save dialogs. Last used open/save paths should be saved and used when opening the dialogs again. There is a Path tab in the Preferences, but there is no predefined path for the molecules files, for the main Open dialog. There is a predefined default path for the script files, which works for the Open... option, but not for the Script Editor. Very illogical! As a whole it is a big nuisance when experimenting with a new script and should open hin files and script files alternatively. 3) Should have been implanted some support for MODELS of pdb files long ago. Recently the program inputs the whole file, every structure one above the other. Because the program does not support the use of MODELS, the input module should read only the first one. Ditto with multiple Sybyl mol2 files. 4) When exporting in Sybyl format, aromatic bonds are consequently assigned to amide bonds (in several versions already). 5) The manual is abundant and generally well written. However, I missed a precise description of the tcl script file commands. There is a very short tutorial only in the pdf manual. Three web url addresses are given as references, two of them are already unavailable, and when trying several commands using the third one, most commands did not function well in Hyperchem. Dr. Tamas E. Gunda Dept. of Pharmaceutical Chemistry University of Debrecen POBox 36 H-4010 Debrecen, Hungary tgunda (AT) puma.unideb.hu ----- Original Message ----- From: "Joe Patrick" To: Sent: Thursday, October 07, 2004 19:17 PM Subject: CCL:HyperChem > Good Day, > > I work for Hypercube, Inc. makers of HyperChem. > > We would like to hear opinoins from CCL in regards to our software. If > you have any experience with or comments about the software, please > contact me at patrick_at_hyper.com. > > Thank you for your time. > > Best Regards, > Joe Patrick > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY_at_ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST_at_ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow:at:nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > >