From chemistry-request@ccl.net Wed Aug 13 05:20:28 2003 Received: from bute.st-andrews.ac.uk (bute.st-and.ac.uk [138.251.12.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7D9KR98021378 for ; Wed, 13 Aug 2003 05:20:28 -0400 Received: from Babydesign.st-andrews.ac.uk (bmspc-glt2-18 [138.251.94.166]) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with ESMTP id KAA28314 for ; Wed, 13 Aug 2003 10:18:13 +0100 (BST) Message-Id: <5.2.0.9.0.20030813101705.00bd3ab8^at^bute.st-andrews.ac.uk> X-Sender: im17^at^bute.st-andrews.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Wed, 13 Aug 2003 10:20:37 +0100 To: chemistry^at^ccl.net From: "Ibrahim M.Moustafa" Subject: Re: Arabinose structure In-Reply-To: <200308130805.KAA12376^at^bisse.novo.dk> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCl users, Thanks for Leif and Rick for their help. The answer of my question was to draw the mirror image and nothing to do with the axial and equatorial positions; axials and equatorials stay as they are. Thanks, Ibrahim At 09:05 13/08/2003, you wrote: >Dear Ibrahim M. Moustafa. > >I suppose you already received answers to your question, >but here is my version: > > The simplest way of drawing the mirror image of a molecule > is by using a mirror - or looking at the drawing from the other > side, if you have it drawn on (semi)transparent paper. > That should also highlight the fact that axial/equatorial > does not vary among mirror forms. > Now, you may not like the orientation you get from the simple > mirror image. In that case you may need some imagination to > draw the molecule in a different perspective. > But bear in mind that axial stays axial etc. > >Sincerely, > >/Leif Norskov > Novo Nordisk A/S > Copenhagen > Denmark > LNL^at^novo.dk > > > Date: Tue, 12 Aug 2003 17:00:56 +0100 > > To: chemistry^at^ccl.net > > From: "Ibrahim M.Moustafa" > > Subject: CCL:Arabinose structure > > > > Dear CCL users, > > > > I have a small question about the stereochemistry representations of > > the pyranoside structure of Arabinose. > > How to draw the chair conformation of the D- and L-forms of Arabinose?. > > > > I'm a bit confused; if I want to draw the pyranoside chair conformation > > (4C1) of the D-form from the Fischer projection in which the > > OH at C2 lies to the left, C3(OH) to the right and C4(OH) to the right, > > I'd draw this chair conformation with: > > > > OH(ax) above the ring at C2, OH(ax) below the ring at C3, and OH(eq) > > below the ring at C4. > > > > Now, If I want to draw the same conformation for the L-form > > (the mirror image of D-form), do I need to alternate the OH groups > > from axial to equatorial and vice versa? > > or how to draw the chair conformation for the L-form? > > > > Appreciated your help. > > > > regards, > > Ibrahim Ibrahim M.Moustafa Centre for Biomolecular Sciences St-Andrews University North Haugh, St-Andrews Fife KY16 9ST Scotland, U.K. Tel. +44 (0)1334 467257 Fax +44 (0)1334 462595 e-mail: im17^at^st-andrews.ac.uk From chemistry-request@ccl.net Tue Aug 12 15:51:06 2003 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7CJp698024373 for ; Tue, 12 Aug 2003 15:51:06 -0400 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3p2/8.9.3) with ESMTP id PAA23797; Tue, 12 Aug 2003 15:51:05 -0400 (EDT) Message-ID: <3F3944E4.477DFA21^at^cornell.edu> Date: Tue, 12 Aug 2003 14:50:09 -0500 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Ru-Zhen Li CC: chemistry^at^ccl.net Subject: Re: CCL:question about BABEL References: <000401c360db$911c2130$402b258a@Ruzhen> Hi all Shouldn't the autoexec.bat file be in the root directory of the c:\ drive? Mine is. Richard Ru-Zhen Li wrote: > [Image] > Dear all Thank you for all the kind people reply to me, and now, I > have done it again from the very beginning, the problem still > exist. 1)I downloaded the babel106.zip from > ftp://www.ccl.net/pub/chemistry/software/UNIX/babel/ 2)I unziped it > and copied the BABEL.EXEL, ELEMENT.LIS, TYPES.LIS to C:\BABEL 3)I add > the SET BABEL_DIR=C:\BABEL to the AUTEXEC.BAT file which is in > C:\Documents and Settings\ezw079.MATDOM\My Documents\My Received > Files\winxpbootdisk\winxpbootdisk\HPWinXPbootdisk\WindowsXP&(&;+&\ 4)I > copied the 1N5U.pdb into C:\BABEL 5)and then I entered the C:\BABEL > under dos typed babel -ip 1N5U.pdb -ocache output.csf nothing > happened, no error, no warning, no output file. and I tried the Open > Babel, but seems that it is under UNIX, not DOS or Windows Thank you > in > advance! regards,Ru-Zhen ********************************************************************** > > Ms Ru-Zhen Li 0044-020-78826327 > r.li^at^qmul.ac.uk > Materials Department > Queen Mary > University of London > E1 4NS -- Richard L. Wood, Ph. D. Physical/Computational Chemist From chemistry-request@ccl.net Wed Aug 13 05:25:31 2003 Received: from mx1.aist.go.jp (mx1.aist.go.jp [150.29.246.133]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7D9PU98021526 for ; Wed, 13 Aug 2003 05:25:31 -0400 Received: from rpsmtp1.aist.go.jp by mx1.aist.go.jp with ESMTP id h7D9PiK0010652; Wed, 13 Aug 2003 18:25:44 +0900 (JST) env-from (masakatsu-ito^at^aist.go.jp) Received: from smtp3.aist.go.jp by rpsmtp1.aist.go.jp with ESMTP id h7D9Pi4U013043; Wed, 13 Aug 2003 18:25:44 +0900 (JST) env-from (masakatsu-ito^at^aist.go.jp) Received: from localhost by smtp3.aist.go.jp with ESMTP id h7D9Ph8L026172; Wed, 13 Aug 2003 18:25:43 +0900 (JST) env-from (masakatsu-ito^at^aist.go.jp) Date: Wed, 13 Aug 2003 18:25:03 +0900 (JST) Message-Id: <20030813.182503.730576284.Masakatsu Ito^at^aist.go.jp> To: jim^at^ks.uiuc.edu Cc: masakatsu-ito^at^aist.go.jp, chemistry^at^ccl.net Subject: Re: CCL:Reusing the NAMD code to build C++ simulation program From: masakatsu-ito^at^aist.go.jp In-Reply-To: References: <20030809.035808.229724605.Masakatsu Ito^at^aist.go.jp> X-Mailer: Mew version 2.3 on XEmacs 21.1.14 (Cuyahoga Valley) Mime-Version: 1.0 Content-Type: Text/Plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Dr. Phillips, Thank you so much for your helpful advice. Now I am planning to rewrite a part of our C++ framework in Charm++ to replace the mainmodule (and main() ?) of the NAMD code with our code. To build a replica exchange molecular dynamics (REMD) or REM simulation, I have to instantiate a set of molecular modeling objects which return a potential energy and force vector as a function of atom positions. I, however, am afraid that a Tcl interpreter does not provide a way for creating a set of namd2 objects to which our framework delegates force field calculations. Thus I am trying to understand which objects in the NAMD code performs the force field calculation and how to instantiate those objects. There are two points in the NAMD code which puzzle me. First, the main() function does not seem to be invoked in the Charm++ execution model, because the Charm++ programming manual says that the Charm Kernel starts the execution by creating a mainchare instance. The manual does not show any example code including a main() function so that I cannot see how a main() behaves in Charm++. The second is the calling logic for force field computation. I think that the Node object is responsible for all the actual calculation as if the functionalities of a main() function for each CPU are divided into its member functions. And the Sequencer object instantiated in the Node seems to integrate the equation of motion to update the atom positions and velocity vectors. Thus, in our code, I would like to set the atom positions at the Patch objects in the Sequencer, to trigger the force field computation, and to get the resultant force vectors from the Patch objects. But I cannot see which member function triggers the force field computation. Could you tell me which member function should I look into? It is exciting for me to look into the NAMD code and to see how its decomposition scheme and load balancing functionality are implemented. I would be very grateful for any hint or pointer to the documents for the NAMD implementation. Sincerely, Masa Masakatsu Ito , Ph.D Grid Technology Research Center National Institute of Advanced Industrial Science and Technology Tsukuba Central 2, Tsukuba, Ibaraki 305-8568 Japan Phone : +81-29-861-5730 Fax : +81-29-861-5301 E-mail masakatsu-ito^at^aist.go.jp URL http://met.sourceforge.net/ From: Jim Phillips Subject: Re: CCL:Reusing the NAMD code to build C++ simulation program Date: Mon, 11 Aug 2003 16:55:18 -0500 (CDT) Message-ID: > Hi, > > We are looking at making NAMD more modular, but it isn't there yet. As > you observe, Charm++ runs through the entire control structure. You might > be able to graft the entire namd2 program into your code as a single large > simulation object by replacing main() in mainfunc.C with your interface. > NAMD has a Tcl interpreter running at the top level that could maybe be > used to accept commands from your framework. Otherwise, it should be > possible to implement REM with a small amount of network code in a NAMD > Tcl script (and possibly some new Tcl commands). Good luck. > > -Jim > > > On Sat, 9 Aug 2003 masakatsu-ito^at^aist.go.jp wrote: > > > Dear Markus, > > > > Thank you for your quick reply. As you wrote, Mindy, > > a sequential version of NAMD, helped me a lot. > > It was easy to reuse and modify its code. ; > > Thus I rephrase my question. Could somebody give me an explanation > > if it is possible to use the NAMD code instead of the Mindy one > > and how to incorporate its Charm++ code into a C++ framework. > > > > From: Markus Dittrich > > Subject: Re: CCL:Reusing the NAMD code to build C++ simulation program > > > > > Dear Masakatsu, > > > > > > The TCBG group does offer an MD code called > > > MINDY which is derived form NAMD source code > > > written solely in C++. Maybe this will be of > > > help to you. > > > > > > http://www.ks.uiuc.edu/Development/MDTools/mindy/ > > > cheers, > > > MARKUS > > > > > > On Fri, 8 Aug 2003 masakatsu-ito^at^aist.go.jp wrote: > > > > > > > Dear CCL'ers, > > > > > > > > I am wondering if it is easy to reuse the NAMD code to build C++ > > > > simulation program. My question might sound strange because NAMD is so > > > > famous for its high extensibility and object-oriented design with > > > > C++. But NAMD is actually coded in Charm++, an extended C++ for > > > > parallelization, so that the problem is that a programmer has to deal > > > > with Charm++ syntax in the NAMD code and its execution model for > > > > parallel computation. So, could somebody give me a brief explanation > > > > how the NAMD code can be incorporated into C++ framework, or if it is > > > > possible. From chemistry-request@ccl.net Wed Aug 13 04:06:03 2003 Received: from smtp.dicp.ac.cn ([159.226.238.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7D86198018692 for ; Wed, 13 Aug 2003 04:06:03 -0400 Received: from wangyan ([159.226.159.204]) by smtp.dicp.ac.cn (8.11.6/8.11.6) with SMTP id h7D86Fl04530 for ; Wed, 13 Aug 2003 16:06:15 +0800 Message-Id: <200308130806.h7D86Fl04530^at^smtp.dicp.ac.cn> From: "wangyan" To: "chemistry^at^ccl.net" Subject: the meanings of the magnitude of the imaginary frequency? X-mailer: Foxmail 4.2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Date: Wed, 13 Aug 2003 16:8:1 +0800 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h7D86398018693 Dear ccler, I want to know whether there is any meanings for the magnitude of the imaginary frequency at the transition state. It is well known that the more the stretching frequency of the zeolitec OH group, the stronger the O-H bond. Is it still suitable for the imaginary frequency ? Does it mean that the transition state which have higher imaginary frequency is more stable than that which have low imaginary frequency ? any information is welcome. thanks in advance. best regards wangyan !!!!!!!!!!!!!!!!wangyan !!!!!!!!!!!!!!!!wangyanemail^at^dicp.ac.cn !!!!!!!!!!!!!!!!!!!!2003-08-13 From chemistry-request@ccl.net Tue Aug 12 20:46:00 2003 Received: from ns.ciac.jl.cn ([202.98.16.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7D0jt98004969 for ; Tue, 12 Aug 2003 20:45:58 -0400 Received: from RsProxy (localhost [127.0.0.1]) by ns.ciac.jl.cn (8.9.1/8.9.1) with SMTP id IAA20427 for ; Wed, 13 Aug 2003 08:51:04 +0800 (CST) Message-Id: <200308130051.IAA20427)at(ns.ciac.jl.cn> Date: Wed, 13 Aug 2003 8:47:15 +0800 From: zwu To: "chemistry)at(ccl.net" Subject: surface energy calculation Organization: ciac X-mailer: FoxMail 4.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h7D0k098004972 Hi, all, Does anybody know the papers or books contain surface energy calculation? In particular on the nanocrystals. Thanks a lot for any message. Best wishes, Sincerely, -- Z. J. Wu ***************************** Prof. Zhijian Wu, Ph.D Key Laboratory of Rare Earth Chemistry and Physics Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 China E-mail: zjwu)at(ciac.jl.cn, zhijw)at(hotmail.com