From chemistry-request@server.ccl.net Tue Nov 12 09:14:24 2002 Received: from bayer143.bayer.com ([192.122.250.143]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACEEOQ02839 for ; Tue, 12 Nov 2002 09:14:24 -0500 Message-Id: <200211121414.gACEEOQ02839@server.ccl.net> Received: by bayer143.bayer.com id JAA22631 (SMTP Gateway 4.2 for chemistry@ccl.net); Tue, 12 Nov 2002 09:14:23 -0500 (EST) Received: by bayer143.bayer.com (Protected-side Proxy Mail Agent-0); Tue, 12 Nov 2002 09:14:23 -0500 (EST) Subject: software to calculate descriptors: petitjean... To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.4 June 8, 2000 From: "Yan Wang" Date: Tue, 12 Nov 2002 09:15:08 -0500 X-MIMETrack: Serialize by Router on MOXANR/US/BAYER(Release 5.0.9a |January 7, 2002) at 11/12/2002 09:14:24 AM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Hello, Do you know any (free) software that can calculate these descriptors: Graph Mass Index Valence Graph Mass Index Gordon Index Needham Atomic Connectivity Index Needham Valence Atomic Connectivity Index Diameter According to Petitjean Radius According to Petitjean Petitjean Index Total Number of Internal Hydrogen Bonds Thank you very much! Yan From chemistry-request@server.ccl.net Tue Nov 12 08:14:44 2002 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACDEiQ01543 for ; Tue, 12 Nov 2002 08:14:44 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Tue, 12 Nov 2002 07:31:43 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Tue, 12 Nov 2002 07:31:17 -0500 From: "Peter Gannett" To: , Cc: , , Subject: Re: CCL:whom to teach what Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline All: This discussion is getting to a different point, I think, but nonetheless a good one. First, the original one, I agree that physical chemistry has the most math, etc., but this does not necessarily mean that physical chemists are all computational chemists. In my mind, it is becoming a field unto itself. The second part of this - part of the value of computational chemistry is that it provides tools useful for all chemists (and other disciplines like biochemists) but only if computational chemists can talk with lab chemists AND lab chemists can talk with computational chemists. This can not be a one sided affair if it is to be productive. My 2 cents. Pete >>> Mihaly Mezei 11/11/02 02:06PM >>> > of chemists, and so on. To a degree, I am plugged in to the experimental > program. "How to talk to the lab chemists" seems to be one of the weaker > points in the academic training of new computational chemists. As the field > becomes increasingly specialized ("a recognizable science"), I wonder how > this connection, important to the industrial side, will be maintained? Hmmm. What about teaching the lab chemists to talk to the computational chemists? Mihaly Mezei, Dept. of Physiology & Biophysics, Mount Sinai School of Medicine Voice: (212) 241-2186 Fax: (212) 860-3369| WWW (MSSM home): http:// adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Nov 12 09:46:40 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACEkdQ03686 for ; Tue, 12 Nov 2002 09:46:40 -0500 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA13354 for ; Tue, 12 Nov 2002 09:46:39 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3DD1144F.364C69B4@cornell.edu> Date: Tue, 12 Nov 2002 09:46:39 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: Re: CCL:whom to teach what References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mihaly Mezei wrote: ... stuff deleted ... > Hmmm. What about teaching the lab chemists to talk to the computational > chemists? > > Mihaly Mezei, > I recently attended a very good talk by a distinguished HHMI researcher in experimental NMR who made a very important point. In his view there are way too many experimental structural biologists who concentrate too much on methodology and structural questions and are not familiar enough with the biological problems involved. They don't have a good grasp of what the significant high-impact questions are in the field to which they apply their technology. Same applies to computational chemistry I think, so this is a universal problem. It is most obvious to us when there is a funding disparity in the two fields. (probably more funding opportunity, for example, in cancer research than for methodological developments in NMR). We can all go about our research thinking that our own discipline is a field of its own with important questions (experimental or not) but what really counts is what other people do with our work. Part of that, of course, is getting the message out about what can be done, but, it's better not to confuse a truely important question with one that is merely interesting. An important question is one that impacts the most people ... not just the narrow segment of folks in our own field. IMHO funding agencies are resonably good at setting overall priorities so learning to talk to folks in better funded fields and letting their questions drive your reseseach is good for everyone (ok flame me). Richard Gillilan MacCHESS, Cornell From chemistry-request@server.ccl.net Tue Nov 12 04:21:13 2002 Received: from oulu.fi ([130.231.240.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAC9LCQ27692 for ; Tue, 12 Nov 2002 04:21:13 -0500 Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by oulu.fi (8.8.5/8.8.5) with ESMTP id LAA16772; Tue, 12 Nov 2002 11:21:03 +0200 (EET) Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by paju.oulu.fi (8.8.5/8.8.5) with ESMTP id LAA03088; Tue, 12 Nov 2002 11:17:28 +0200 (EET) Date: Tue, 12 Nov 2002 11:17:28 +0200 (EET) From: =?ISO-8859-1?Q?Atte_Sillanp=E4=E4?= X-X-Sender: asillanp@paju.oulu.fi Reply-To: chemistry@ccl.net To: chenghuiqc cc: chemistry@ccl.net Subject: Re: CCL:change the PCM atom radii in Gaussian98 In-Reply-To: <20021110144511.7813.qmail@sina.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 10 Nov 2002, chenghuiqc wrote: > Dear Sir, > > I am using the PCM model in Gaussian98 to study some solvent > effects in a reaction, but I find that I can not use "alpha=1.3" to > change the radii of the atom as the instruction of the gaussian > help.Who can tell me how I can change the radii? Thank you. I have experienced similar problems. I have not been able to change any radii in the SCRF-calculations. Further, it seems, that the read -option in the #-line causes the program to read _only_ the two first lines in the additional section after molecule specification. Is this a known 'feature' and is there a workaround? Here are two example inputs. The first results in radii=bondii, tsnum=100, ret=0.2 (=default) The second: radii=UATM (default), tsum=100, ret=100 In both cases the IOP's are identical, that is, the SCRF-part gets its information via some other route, and thus, modifying it does not help? 1) #P rhf/3-21G** scf=tight scrf(cosmo,solvent=water,read) ... tsnum=100 radii=bondii ret=100 2) #P rhf/3-21G** scf=tight scrf(cosmo,solvent=water,read) ... ret=100 tsnum=100 radii=bondii Any suggestions and explanations are most welcome. All the best, Atte atte.sillanpaa@oulu.fi +358 (0)8 553 1681 (work), KE 368 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) Po-BOX 3000 FIN-90014 University of Oulu FINLAND | Entropy requires no maintenance. | From chemistry-request@server.ccl.net Tue Nov 12 03:23:24 2002 Received: from suncom.rz.hu-berlin.de ([141.20.1.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAC8NNQ25919 for ; Tue, 12 Nov 2002 03:23:24 -0500 Received: from impact1.chemie.hu-berlin.de (impact1.chemie.hu-berlin.de [141.20.72.25]) by suncom.rz.hu-berlin.de (8.9.3/8.9.3) with ESMTP id JAA20522; Tue, 12 Nov 2002 09:23:22 +0100 (MET) Received: (from ah@localhost) by impact1.chemie.hu-berlin.de (SGI-8.9.3/8.9.3) id JAA58010; Tue, 12 Nov 2002 09:23:21 +0100 (MEZ) Date: Tue, 12 Nov 2002 09:23:21 +0100 From: "Dr. Alexander Hofmann" To: CHEMISTRY@ccl.net Subject: Summary - G98/Linux and huge files Message-ID: <20021112092321.H397459@chemie.hu-berlin.de> Reply-To: ah@chemie.hu-berlin.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i Hi, here is the summary of all responses to my question, Thanks a lot to all contributers! The question was: Are there possibilities to circumvent the 2 GB limit with Gaussian 98 under Linux (Suse 8.0 2.4.x Kernel). I know the rwf-splitting. My aim is to write really huge files (like 100 GB or so). I haven't succeeded to write more than 16 Gb in total. (8x2 Gb), although I've tried. Answer: Shortly, the answer is no within quotation marks. There are possible attempts to circumvent it by using new gcc-libs (>3.1) to reach 16 GB in one file. But anyway, you can't go beyond because of 32bit addressing. Douglas J. Fox suggested to build a 64bit exe on the 32bit system, if there is no way to reach a real 64bit machine. The performance is expected to be very bad. Thanks again. Alex PS: The answers of all contributors Gaussian is really messy, changing something usually means breaking something else. -- Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Yes, it is possible to cross 2GB file limit under Linux. You need to install new GNU GCC version (3.1 or latest) to enable large files support with g77 Fortran compiler. I have not tryed it with G98, but GCC 3.1 recompiled GAMESS works fine. But I'm insure that you really could run such a big tasks on 32-bit platform due to other (say, maximum array index, etc) restrictions. -- Best regards, Gregory Shamov, Dept. Chemistry Kazan State University mailto:gas5x@bancorp.ru Dear, Alexander, We recently build LINDA parallel version of g98 with large file support(LFS). Now we can make scratch file of >2GB without file splitting. You will get information on how to build g98 with LFS at our page http://ruby.ch.wani.osaka-u.ac.jp/QC.html But, there is still 16GB limit because this is due to limitation of 32 bit integ er used in g98. We do not intend to challenge this problem at present because it is time -consuming job and the resulting build must be well-tested. ---------------------------------------------------- Koichi Nozaki, Dr. Department of Chemistry, Graduate School of Science, Osaka university TEL: 06-6850-5777 / FAX: 06-6850-5785 Hi, I have a patch that will enable 16GB file segments for g98/Linda on Linux. At first you might think there's no advantage to it, since it's possible to split the RWF into eight 2GB segments. However, it's not possible to split the file used by the Linda workers. So the patch at least enables 16GB for the worker processes. I can send it to you if you like. It used to be posted on a Web site (not mine) until Gaussian, Inc. requested that it be removed. Perhaps because the method was not certified to produce correct results. As far as using files >16GB, that will require a more thorough conversion of integers to 64-bit. I haven't yet been successful yet in getting this to work on Linux. I've also been told that even if it did work, the effect on the performance would be devastating, perhaps a factor of 10. Anyway, if you're successful in using large files >16GB, please let me know... Bryan -- Bryan Putnam, IT Research Computing Services Mathematical Sciences Building Email: bfp@purdue.edu 150 North University Street Phone: 765.496.8225 West Lafayette, IN 47907-2068 Fax: 765.494.0566 http://www.purdue.edu/ITaP http://www-rcd.cc.purdue.edu/~bfp/ Dr. Hofmann, The short answer is no, there is no option in G98 to do this. The situation is that because the Intel Pentium of processors are 32 bit processors, g98 is configured as a 32 bit application. Using larger word lengths for disk addresses would require promoting all integers in G98 to be 64 bits. We have not done the experiment but for systems with 64 bit hardware where we previously had g98 configured as a 32 bit application we see a 10-15% performance decrease on going to 64 bits. Doing all of the integer manipulations in Gaussian, as would be required to make it a 64 bit application on a 32 bit platform, would be catastrophic to performance. Perhaps not a bad trade for small applications but assuming you want 100GB of disk you need every ounce of performance you can get. If you are doing large, conventional post-HF methods you will need a platform with 64 bit arithmetic throughout. At this point the Alpha Linux systems are an option. We also have the first generation Itanium but price performance is not so great. We hope to have Itanium2 early next year with our next release. -- Douglas J. Fox Technical Support Gaussian, Inc. help@gaussian.com -- Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie Arbeitsgruppe Quantenchemie Brook-Taylor-Strasse 2 12489 Berlin ah@chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35 From chemistry-request@server.ccl.net Tue Nov 12 04:17:13 2002 Received: from mailgate.rz.uni-karlsruhe.de ([129.13.64.97]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAC9HCQ27261 for ; Tue, 12 Nov 2002 04:17:13 -0500 Received: from rz70.rz.uni-karlsruhe.de (rz70.rz.uni-karlsruhe.de [129.13.97.243]) by mailgate.rz.uni-karlsruhe.de with esmtp (Exim 3.36 #1) id 18BXAP-0006Hn-00; Tue, 12 Nov 2002 10:17:06 +0100 Date: Tue, 12 Nov 2002 10:17:05 +0100 (CET) From: Harald Svedung To: Mihaly Mezei cc: Stephen Bowlus , "'James Robinson'" , , "Dr. Daniel Glossman-Mitnik" Subject: Re: CCL:whom to teach what In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id gAC9HDQ27264 Hi there! I'm not an expert in the development of languages, but I think the question is important, interesting and general. The common domain of consepts should be cared fore, developed and tought. There is a theoretical development and practical usefulness of concepts by all actors. With a new "recognizable" (read self-contained?) science we need lines of communication. After all, we share this planet together! :-) /Harald On Mon, 11 Nov 2002, Mihaly Mezei wrote: > > of chemists, and so on. To a degree, I am plugged in to the experimental > > program. "How to talk to the lab chemists" seems to be one of the weaker > > points in the academic training of new computational chemists. As the field > > becomes increasingly specialized ("a recognizable science"), I wonder how > > this connection, important to the industrial side, will be maintained? > > Hmmm. What about teaching the lab chemists to talk to the computational > chemists? > > Mihaly Mezei, > > Dept. of Physiology & Biophysics, Mount Sinai School of Medicine > Voice: (212) 241-2186 Fax: (212) 860-3369| > WWW (MSSM home): http:// > adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > Dr. Harald Svedung cellphone: +49-175 736 2576 Institut für Physikalische Chemie or: +46-709-223 206 Universität Karlsruhe Fritz-Haber-Weg 4 D-761 28 Karlsruhe Tyskland Tel: +49-721 608 2715 Fax:+49-721 608 6524 From chemistry-request@server.ccl.net Tue Nov 12 00:30:45 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAC5UjQ22846 for ; Tue, 12 Nov 2002 00:30:45 -0500 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id AAA10710; Tue, 12 Nov 2002 00:30:43 -0500 (EST) Message-ID: <3DD091FB.94083ADC@cornell.edu> Date: Mon, 11 Nov 2002 23:30:35 -0600 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: "chemistry@ccl.net" Subject: Re: CCL:whom to teach what References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I wonder what courses these "computational chemists" took that I didn't take... Richard Mihaly Mezei wrote: > > of chemists, and so on. To a degree, I am plugged in to the experimental > > program. "How to talk to the lab chemists" seems to be one of the weaker > > points in the academic training of new computational chemists. As the field > > becomes increasingly specialized ("a recognizable science"), I wonder how > > this connection, important to the industrial side, will be maintained? > > Hmmm. What about teaching the lab chemists to talk to the computational > chemists? > > Mihaly Mezei, > > Dept. of Physiology & Biophysics, Mount Sinai School of Medicine > Voice: (212) 241-2186 Fax: (212) 860-3369| > WWW (MSSM home): http:// > adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Richard L. Wood, Ph. D. Physical/Computational Chemist From chemistry-request@server.ccl.net Tue Nov 12 11:47:51 2002 Received: from fort-point-station.mit.edu ([18.7.7.76]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACGloQ11257 for ; Tue, 12 Nov 2002 11:47:50 -0500 Received: from grand-central-station.mit.edu (GRAND-CENTRAL-STATION.MIT.EDU [18.7.21.82]) by fort-point-station.mit.edu (8.9.2/8.9.2) with ESMTP id LAA02454 for ; Tue, 12 Nov 2002 11:47:50 -0500 (EST) Received: from manawatu-mail-centre.mit.edu (MANAWATU-MAIL-CENTRE.MIT.EDU [18.7.7.71]) by grand-central-station.mit.edu (8.9.2/8.9.2) with ESMTP id LAA15318 for ; Tue, 12 Nov 2002 11:47:50 -0500 (EST) Received: from department-of-alchemy.mit.edu (DEPARTMENT-OF-ALCHEMY.MIT.EDU [18.7.16.69]) by manawatu-mail-centre.mit.edu (8.9.2/8.9.2) with ESMTP id LAA28817 for ; Tue, 12 Nov 2002 11:47:49 -0500 (EST) Received: from localhost (damians@localhost) by department-of-alchemy.mit.edu (8.9.3) with ESMTP id LAA23621; Tue, 12 Nov 2002 11:47:49 -0500 (EST) Date: Tue, 12 Nov 2002 11:47:49 -0500 (EST) From: Damian A Scherlis Perel To: Subject: trouble with large calculations in G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: Hi, I'm trying to perform MP2 calculations on some big system, but Gaussian stops with the following lines at the end of the log file: Disk-based method using O(N**2) memory for 9 occupieds at a time. Estimated scratch disk usage= 1557843486 words. IMap= 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 IMap= 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 IMap= 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 IMap= 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 IMap= 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 Actual scratch disk usage= 1555753214 words. Erroneous write during file extend. write 32767 instead of 4096 Probably out of disk space. However, the disk where I write the scratch files is only 20% full or less. Is there any way to prevent this stop from happening? Thanks a lot, ------------------------ Damian Scherlis Department of Materials Science & Engineering Massachusetts Institute of Technology damians@mit.edu 617 253 6026 From chemistry-request@server.ccl.net Tue Nov 12 10:58:17 2002 Received: from wrzx35.rz.uni-wuerzburg.de ([132.187.3.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACFwGQ09917 for ; Tue, 12 Nov 2002 10:58:16 -0500 Received: from wrzx30.rz.uni-wuerzburg.de (wrzx30.rz.uni-wuerzburg.de [132.187.1.30]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.05) with ESMTP id QAA17040; Tue, 12 Nov 2002 16:58:13 +0100 (MET) Received: from localhost (localhost [127.0.0.1]) by virusscan.rz.uni-wuerzburg.de (Postfix) with ESMTP id B622B4F8; Tue, 12 Nov 2002 16:56:58 +0100 (CET) Received: from wrzx07.rz.uni-wuerzburg.de (wrzx07.rz.uni-wuerzburg.de [132.187.1.7]) by wrzx30.rz.uni-wuerzburg.de (Postfix) with ESMTP id 8BF304D7; Tue, 12 Nov 2002 16:56:58 +0100 (CET) Received: from imap.uni-wuerzburg.de (wrzx31.rz.uni-wuerzburg.de [132.187.3.31]) by wrzx07.rz.uni-wuerzburg.de (Postfix) with ESMTP id 7D9B3734; Tue, 12 Nov 2002 16:56:58 +0100 (CET) Received: from localhost (wrzx32.rz.uni-wuerzburg.de [132.187.3.32]) by imap.uni-wuerzburg.de (Postfix) with ESMTP id 1EF174F9; Tue, 12 Nov 2002 16:56:58 +0100 (CET) Received: from 132.187.70.201 ( [132.187.70.201]) as user phar072@132.187.3.41 by webmail.uni-wuerzburg.de with HTTP; Tue, 12 Nov 2002 16:56:58 +0100 Message-ID: <1037116618.3dd124ca0f847@webmail.uni-wuerzburg.de> Date: Tue, 12 Nov 2002 16:56:58 +0100 From: Nikolaus Stiefl To: Yan Wang Cc: chemistry@ccl.net Subject: Re: CCL:software to calculate descriptors: petitjean... References: <200211121414.gACEEOQ02839@server.ccl.net> In-Reply-To: <200211121414.gACEEOQ02839@server.ccl.net> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 132.187.70.201 X-Virus-Scanned: by AMaViS (Rechenzentrum Universitaet Wuerzburg) Hi, I think you might want to try DRAGON by Roberto Todeschini et al: http://www.disat.unimib.it/chm/Dragon.htm Dragon is able to calculate 1481 molecular descriptors, it has a nice interface, runs on Windows PC's, is very fast and is for free (as far as I know). I am not sure if it calculates all the mentioned descriptors, but I think it should do for at least some of them. Nik -- Nikolaus Stiefl Chemometriks and Drug Design University Wuerzburg Dept. of Pharmacy Am Hubland D-97074 Wuerzburg Germany Phone: +49 - 931 8885473 Zitat von Yan Wang : > Hello, > > Do you know any (free) software that can calculate these descriptors: > Graph Mass Index > Valence Graph Mass Index > Gordon Index > Needham Atomic Connectivity Index > Needham Valence Atomic Connectivity Index > Diameter According to Petitjean > Radius According to Petitjean > Petitjean Index > Total Number of Internal Hydrogen Bonds > > Thank you very much! > > Yan > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > > From chemistry-request@server.ccl.net Tue Nov 12 11:50:11 2002 Received: from facstaff.wesleyan.edu ([129.133.1.61]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACGoAQ11302 for ; Tue, 12 Nov 2002 11:50:11 -0500 Received: from wesleyan.edu (ion.chem.wesleyan.edu [129.133.89.89]) by facstaff.wesleyan.edu (8.11.2/8.10.2) with ESMTP id gACGo7u12286 for ; Tue, 12 Nov 2002 11:50:07 -0500 (EST) Message-ID: <3DD13011.2050607@wesleyan.edu> Date: Tue, 12 Nov 2002 11:45:05 -0500 From: Surjit Dixit Reply-To: sdixit@wesleyan.edu Organization: Wesleyan University User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.0) Gecko/20020529 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:whom to teach what References: <3DD091FB.94083ADC@cornell.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-ECS-MailScanner: Found to be clean I am not sure if we are taught anywhere about "how to talk to a 'scientist from such and such a field'". I guess the talent to "talk" is something each individual develops to different degree depending on their own interest and approach to the problem at hand. We were watching the dramatised version of the times before the discovery of DNA structure in the film "The Race to the Double Helix" yesterday. The Watson and Crick achievment was greatly driven by their ability to "talk", grasp and appreciate all the various bits of information about DNA that was floating around in the various communities. Whosoever may do the talking, the result is good for science. The need to talk is crucial for researchers in any field if they wish to answer the "big" questions and get the usefulness of their work appreciated by the other community. This becomes especially true for the computational chemist, since our field is the new-comer and is demanding the recognition. Surjit Dr. Richard L. Wood wrote: >I wonder what courses these "computational chemists" took that I didn't take... > >Richard > >Mihaly Mezei wrote: > > > >>>of chemists, and so on. To a degree, I am plugged in to the experimental >>>program. "How to talk to the lab chemists" seems to be one of the weaker >>>points in the academic training of new computational chemists. As the field >>>becomes increasingly specialized ("a recognizable science"), I wonder how >>>this connection, important to the industrial side, will be maintained? >>> >>> >>Hmmm. What about teaching the lab chemists to talk to the computational >>chemists? >> >>Mihaly Mezei, >> >>Dept. of Physiology & Biophysics, Mount Sinai School of Medicine >> Voice: (212) 241-2186 Fax: (212) 860-3369| >> WWW (MSSM home): http:// >> adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01 >> WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei >> >> >> > >-- >Richard L. Wood, Ph. D. >Physical/Computational Chemist > > > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > > > From chemistry-request@server.ccl.net Tue Nov 12 12:14:59 2002 Received: from wrzx35.rz.uni-wuerzburg.de ([132.187.3.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACHExQ12153 for ; Tue, 12 Nov 2002 12:14:59 -0500 Received: from wrzx30.rz.uni-wuerzburg.de (wrzx30.rz.uni-wuerzburg.de [132.187.1.30]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.05) with ESMTP id SAA19661 for ; Tue, 12 Nov 2002 18:14:58 +0100 (MET) Received: from localhost (localhost [127.0.0.1]) by virusscan.rz.uni-wuerzburg.de (Postfix) with ESMTP id 7C99748A for ; Tue, 12 Nov 2002 18:14:58 +0100 (CET) Received: from wrzx07.rz.uni-wuerzburg.de (wrzx07.rz.uni-wuerzburg.de [132.187.1.7]) by wrzx30.rz.uni-wuerzburg.de (Postfix) with ESMTP id 721C23DB for ; Tue, 12 Nov 2002 18:14:58 +0100 (CET) Received: from imap.uni-wuerzburg.de (wrzx31.rz.uni-wuerzburg.de [132.187.3.31]) by wrzx07.rz.uni-wuerzburg.de (Postfix) with ESMTP id 6098B767 for ; Tue, 12 Nov 2002 18:14:58 +0100 (CET) Received: from localhost (wrzx32.rz.uni-wuerzburg.de [132.187.3.32]) by imap.uni-wuerzburg.de (Postfix) with ESMTP id 536464F9 for ; Tue, 12 Nov 2002 18:14:58 +0100 (CET) Received: from 132.187.70.201 ( [132.187.70.201]) as user phar072@132.187.3.41 by webmail.uni-wuerzburg.de with HTTP; Tue, 12 Nov 2002 18:14:58 +0100 Message-ID: <1037121298.3dd13712472b1@webmail.uni-wuerzburg.de> Date: Tue, 12 Nov 2002 18:14:58 +0100 From: Nikolaus Stiefl To: chemistry@ccl.net Subject: software for ligand-receptor interaction energy evaluation ? MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 132.187.70.201 X-Virus-Scanned: by AMaViS (Rechenzentrum Universitaet Wuerzburg) Hi, a colleague of mine asked me if I could calculate interaction energies between a ligand and a receptor into which he docked some compounds. I had a look at some of the complexes and it seems like he wants to use this for a reevaluation of the activity of his docked structures. Unfortunately I am not too much into this sort of energy calculations and now I am looking for a freeware program that is able to do that with not too much effort. I would be very grateful if anybody could point me into a direction. Cheers Nik -- Nikolaus Stiefl Chemometriks and Drug Design University Wuerzburg Dept. of Pharmacy Am Hubland D-97074 Wuerzburg Germany Phone: +49 - 931 8885473 From chemistry-request@server.ccl.net Tue Nov 12 12:12:37 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACHCaQ12029 for ; Tue, 12 Nov 2002 12:12:36 -0500 Received: from tempest.sd.lionbioscience.com (tempest.sd.lionbioscience.com [10.8.0.8]) by so.sd.lionbioscience.com (8.11.3/8.11.3) with ESMTP id gACHBtg21962; Tue, 12 Nov 2002 09:11:55 -0800 (PST) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Tue, 12 Nov 2002 09:11:55 -0800 Message-ID: From: Stephen Bowlus To: "'Mihaly Mezei'" Cc: "'James Robinson'" , chemistry@ccl.net, "Dr. Daniel Glossman-Mitnik" Subject: RE: whom to teach what Date: Tue, 12 Nov 2002 09:11:49 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C28A6E.968DDB70" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C28A6E.968DDB70 Content-Type: text/plain; charset="iso-8859-1" I don't think there is a large barrier to the lab chemist learning what is necessary of the computational chemist's lexicon. There is a large number of researchers who crossed over from the experimental to the computational side (the dark side ...) at some time in their careers. This might, in fact, apply to a majority of "industrial" modellers, computational chemists, and informatics workers who started out in the late 70's or early 80's. And many who have made the crossing back-and-forth several times! BUT (!) chemistry is fundamentally an experimental science. It behooves the numerically-minded to recognize a common view is that the best simulations and models are so much hand-waving until they are tested and validated by experiment. Certainly as a modeler, my primary function is to design experiments. So I darn well better understand the limitations of the experimental techniques and materials available to the wet-lab people, their motivations, etc., etc. This is not to say that wet-lab chemists should not have additional grounding in the appropriate application of computational techniques. Or a much better acquaintance with experimentally-oriented topics like statistics (ignorance here being the bane of the QSAR specialist's existence). But I believe the onus is on the computational chemist to bridge that gap. We simulate nature, and we need to convince our lab brethren of the fidelity of that simulation. When they see it works (well, better than random ...), they do go that extra distance, and begin to incorporate the necessary concepts into their planning. ...IMHO ... >> > > of chemists, and so on. To a degree, I am plugged in to > the experimental > > program. "How to talk to the lab chemists" seems to be one > of the weaker > > points in the academic training of new computational > chemists. As the field > > becomes increasingly specialized ("a recognizable > science"), I wonder how > > this connection, important to the industrial side, will be > maintained? > > Hmmm. What about teaching the lab chemists to talk to the > computational > chemists? > > Mihaly Mezei, > > ------_=_NextPart_001_01C28A6E.968DDB70 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: whom to teach what

I don't think there is a large barrier to the lab = chemist learning what is necessary of the computational chemist's = lexicon.  There is a large number of researchers who crossed over = > from the experimental to the computational side (the dark side ...) at = some time in their careers.  This might, in fact, apply to a = majority of "industrial" modellers, computational chemists, = and informatics workers who started out in the late 70's or early = 80's.  And many who have made the crossing back-and-forth several = times!

BUT (!) chemistry is fundamentally an experimental = science.  It behooves the numerically-minded to recognize a common = view is that the best simulations and models are so much hand-waving = until they are tested and validated by experiment.  Certainly as a = modeler, my primary function is to design experiments.  So I darn = well better understand the limitations of the experimental techniques = and materials available to the wet-lab people, their motivations, etc., = etc.

This is not to say that wet-lab chemists should not = have additional grounding in the appropriate application of = computational techniques.  Or a much better acquaintance with = experimentally-oriented topics like statistics (ignorance here being = the bane of the QSAR specialist's existence).  But I believe the = onus is on the computational chemist to bridge that gap.  We = simulate nature, and we need to convince our lab brethren of the = fidelity of that simulation.  When they see it works (well, better = than random ...), they do go that extra distance, and begin to = incorporate the necessary concepts into their planning.

...IMHO ...

>>
> > of chemists, and so on.  To a degree, = I am plugged in to
> the experimental
> > program.  "How to talk to the = lab chemists" seems to be one
> of the weaker
> > points in the academic training of new = computational
> chemists.  As the field
> > becomes increasingly specialized ("a = recognizable
> science"), I wonder how
> > this connection, important to the = industrial side, will be
> maintained?
>
> Hmmm. What about teaching the lab chemists to = talk to the
> computational
> chemists?
>
> Mihaly Mezei,
>
>

------_=_NextPart_001_01C28A6E.968DDB70-- From chemistry-request@server.ccl.net Tue Nov 12 13:32:43 2002 Received: from bonaire.server1.odu.edu ([128.82.224.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACIWhQ14405 for ; Tue, 12 Nov 2002 13:32:43 -0500 Received: from amethyst.ts.odu.edu (amethyst.ts.odu.edu [128.82.225.33]) by bonaire.server1.odu.edu (8.12.5/8.12.3) with ESMTP id gACIWcwd013417 for ; Tue, 12 Nov 2002 13:32:39 -0500 (EST) Subject: IPCM convergence problems To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.9 November 16, 2001 Message-ID: From: "Jennifer L Radkiewicz" Date: Tue, 12 Nov 2002 13:45:19 -0500 X-MIMETrack: Serialize by Router on Amethyst/Servers/ODU(Release 5.0.9a |January 7, 2002) at 11/12/2002 01:32:14 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Dear all, I am having trouble using the IPCM method in Gaussian98 and have been unable to get a response from Gaussian itself. One single point job uses IPCM with MP2/6-311G** and MP2/6-31G* optimized gas phase geometries. The calculation eventually reaches a point where the MaxDiff starts to diverge during the Tomasi Approximation II section. The energy had been steadily decreasing up until this point. Three other calculations done on the same molecule but different conformations had no problem converging. Does anyone know a way to correct this problem? For another system, I am again having problems with IPCM. This time with B3LYP/6-31+G*. In this case, the calculation appears to get stuck in a loop and does not converge. There was no problem with these calculations when B3LYP/6-31G* was used. Any suggestions? Thank you for any help you can provide, Jennifer Radkiewicz Assistant Professor Old Dominion University jradkiew@odu.edu From chemistry-request@server.ccl.net Tue Nov 12 15:35:54 2002 Received: from sims.csuohio.edu ([137.148.5.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACKZrQ17210 for ; Tue, 12 Nov 2002 15:35:53 -0500 Received: from csuohio.edu (titanium.asic.csuohio.edu [137.148.208.32]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0H5H002K9D99WA@sims.csuohio.edu> for chemistry@server.ccl.net; Tue, 12 Nov 2002 15:36:45 -0500 (EST) Date: Tue, 12 Nov 2002 15:35:52 -0500 From: Valentin Gogonea Subject: CHelpG calculation for Fe To: chemistry@server.ccl.net Message-id: <55F016AA-F67E-11D6-9403-003065CDB448@csuohio.edu> MIME-version: 1.0 X-Mailer: Apple Mail (2.548) Content-type: text/plain; format=flowed; charset=US-ASCII Content-transfer-encoding: 7BIT Dear CCLers: Can anybody give me a suggestion of what radius should I use for Fe(2+) and Fe(3+) to do CHelpG calculations with gaussian98? Thank you. Valentin Gogonea Cleveland State University From chemistry-request@server.ccl.net Tue Nov 12 15:30:29 2002 Received: from srvus010.unitedcatalysts.com ([208.23.162.8]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gACKUTQ17096 for ; Tue, 12 Nov 2002 15:30:29 -0500 Received: from 10.1.0.105 by srvus010.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Tue, 12 Nov 2002 15:29:50 -0500 Received: by lvlxch02.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id ; Tue, 12 Nov 2002 15:30:29 -0500 Message-ID: <5CF08BBFE6DE97478C1E76E654CAF908221008@lvlxch02.unitedcatalysts.com> From: "Shobe, Dave" To: chemistry@ccl.net Subject: RE: whom to teach what Date: Tue, 12 Nov 2002 15:30:28 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gACKUTQ17099 On Mon, 11 Nov 2002, Mihaly Mezei wrote: > > of chemists, and so on. To a degree, I am plugged in to the experimental > > program. "How to talk to the lab chemists" seems to be one of the weaker > > points in the academic training of new computational chemists. As the field > > becomes increasingly specialized ("a recognizable science"), I wonder how > > this connection, important to the industrial side, will be maintained? > > Hmmm. What about teaching the lab chemists to talk to the computational > chemists? > Yes, I think 2-way communication would be useful. :-) --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. From chemistry-request@server.ccl.net Tue Nov 12 18:49:45 2002 Received: from handler1.mail.rice.edu ([128.42.58.201]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACNniQ21510 for ; Tue, 12 Nov 2002 18:49:44 -0500 Received: from localhost (localhost [127.0.0.1]) by handler1.mail.rice.edu (Postfix) with SMTP id 5446EE4464; Tue, 12 Nov 2002 17:49:45 -0600 (CST) Received: from localhost (localhost [127.0.0.1]) by handler1.mail.rice.edu (Postfix) with ESMTP id 0EC9FE44B1; Tue, 12 Nov 2002 17:49:45 -0600 (CST) Received: from spca.ruf.rice.edu (spca.ruf.rice.edu [128.42.31.11]) by handler1.mail.rice.edu (Postfix) with ESMTP id 6BF51E4464; Tue, 12 Nov 2002 17:49:44 -0600 (CST) Received: from localhost (kostya@localhost) by spca.ruf.rice.edu (8.9.0/8.9.0) with ESMTP id RAA25990; Tue, 12 Nov 2002 17:49:44 -0600 (CST) Date: Tue, 12 Nov 2002 17:49:43 -0600 (CST) From: "Konstantin N. Kudin" X-X-Sender: To: Connie Chang Cc: Subject: Re: Questions about SCF convergence again with Gaussian98W and Hyperchem In-Reply-To: <3DCBFEF5.39A4EF95@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS snapshot-20020300 X-DCC--Metrics: handler1.mail.rice.edu 1066; Body=1 Fuz1=1 Fuz2=1 Connie, The main issue with the SCF convergence for a large charged molecule is appearance of charge waves. During the SCF charge oscillates from one end of the large molecule to another without ever converging. Using low accuracy SCF options aggrevates the situation - charge waves appear during even earlier cycles of the SCF procedure. It seems like level shifting could be helpful here. Even though you will have to play with it a little to make it work. You might want to start > from a neutral molecule, converge it, and then use level shift for the charged system. Level shift might even help to get the next optimization step right - otherwise you will have to do this step by step ... Larger geometry steps will converge worse than smaller (later) ones. Now, there is a very robust SCF convergence method out there called EDIIS which cures this sort of problems. Unfortunately, as far as I know it is not yet available in commercial software packages so you will have to wait a little before you can use it. Here is the reference: K.N.Kudin, G.E.Scuseria and E. Cances, J.Chem.Phys. 116, 8255 (2002). Good luck! Konstantin On Fri, 8 Nov 2002, Connie Chang wrote: > Hi everyone -- > > thank you for all your good suggestions... > > I'm still having trouble getting an optimization and frequency > calculation to work for a charged molecule with 120 atoms. I've tried > with both Hyperchem and Gaussian98W using the PM3 method. And I've > tried some fo the suggestions given by listmembers such as increasing > the maximum number of iterations to 500, setting scf=sleazy, setting > scf=qc, etc... I still get the UNABLE TO ACHIEVE SELF CONSISTENCE error > after (at most) one optimization step. So the energy will converge > once, it moves the atoms by a little bit for the optimization and the > energy fails to converge. > > I have the same problem with hyperchem. Hyperchem does the neutral case > just fine, but as soon as I add a charge of -1 and a multiplicity of 2, > the energy does not even get close to something reasonable (it's large > and positive). > > Does anyone have any further suggestions on what I can do to get either > of the programs to work? Hyperchem does work for a smaller molecule > (~70 atoms), but Gaussian does not. Does the size of the molecule make > it more difficult for these programs and methods to find the minimum > energy? I tried a charged water molecule in Gaussian and it worked > fine.... > > thanks. > Connie > > > From chemistry-request@server.ccl.net Tue Nov 12 14:08:31 2002 Received: from kelly.bath.ac.uk ([138.38.32.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACJ8UQ15386 for ; Tue, 12 Nov 2002 14:08:30 -0500 Received: from mmdf by kelly.bath.ac.uk with pleasure id 18BgOj-00073I-01 for chemistry@ccl.net; Tue, 12 Nov 2002 19:08:29 +0000 Received: from midge.bath.ac.uk ([138.38.32.34] ident=mmdf) by kelly.bath.ac.uk with smtp id 18BgOj-0007vx-01; Tue, 12 Nov 2002 19:08:29 +0000 Received: from prpcn144 ( prpc-n144.bath.ac.uk [138.38.128.144] ) by bath.ac.uk id aa29978 ; 12 Nov 2002 19:08 +0000 From: James Robinson To: chemistry@ccl.net Subject: Whom to teach what continued... young pretenders or experienced hands.. Date: Tue, 12 Nov 2002 19:10:36 -0000 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0000_01C28A7F.2E380C60" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0000_01C28A7F.2E380C60 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit So the debate continues. Most people seem to agree with the general principle that Computational chemistry/Molecular modelling (change description to suit personal taste) is a science in its own right. The scientists doing the computational work need to communicate effectively and understand exactly what is required (yes, no, 18 digit numbers, pretty pictures…) So if starting from scratch, say you grabbed some unsuspecting student and tried to teach them… where would you start? Is there a general foundation to it all? (If only Charles Babbage and Erwin Schrodinger had email addresses..) The people I have met tended to do first degrees in science, computer sciences or maths and then moved into computational chemistry through jobs in industry/academia and postgraduate study. So there is an added advantage. They have experience of real science before attempting the computation. Is the best way, through experience and evolution or would it actually be okay to do it from scratch at the age of 18 or so… With higher education becoming more expensive, I am sure the delight of market forces will influence trends, .. science graduates will become rarer.. unless salaries increase.. new modellers will have to come from somewhere… That’s my 2 pence concluded. j ------=_NextPart_000_0000_01C28A7F.2E380C60 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable So the debate continues

So the debate continues. Most people seem to agree with the general = principle that Computational chemistry/Molecular modelling (change description to suit personal taste) is a science in its own right. The scientists doing the computational work need to communicate effectively and understand = exactly what is required (yes, no, 18 digit numbers, pretty pictures…) =

 

So if starting from scratch, say you grabbed some unsuspecting student and = tried to teach them… where would you start? Is there a general = foundation to it all? (If only Charles Babbage and Erwin Schrodinger had email addresses..) =  The people I have met tended to = do first degrees in science, computer sciences or maths and then moved into = computational chemistry through jobs in industry/academia and postgraduate study. So = there is an added advantage. They have experience of real science before = attempting the computation.

 

Is the best way, through experience and evolution or would it actually be = okay to do it from scratch at the age of 18 or so… =

 

With higher education becoming more expensive, I am sure the delight of = market forces will influence trends, .. science graduates will become rarer.. = unless salaries increase.. new modellers will have to come from = somewhere…

 

That’s my 2 pence concluded. j <= /p>

------=_NextPart_000_0000_01C28A7F.2E380C60-- From chemistry-request@server.ccl.net Tue Nov 12 13:50:25 2002 Received: from fulcrum.physbio.mssm.edu ([146.203.4.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACIoOQ14849 for ; Tue, 12 Nov 2002 13:50:25 -0500 Received: from mezei (helo=localhost) by fulcrum.physbio.mssm.edu with local-esmtp (Exim 3.11 #1) id 18Bg6e-007n9I-00; Tue, 12 Nov 2002 13:49:48 -0500 Date: Tue, 12 Nov 2002 13:49:48 -0500 From: Mihaly Mezei X-X-Sender: mezei@fulcrum.physbio.mssm.edu To: Stephen Bowlus cc: "'James Robinson'" , Computationl Chemistry List , "Dr. Daniel Glossman-Mitnik" Subject: Re: CCL:whom to teach what In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Mihaly Mezei > BUT (!) chemistry is fundamentally an experimental science. It behooves the > numerically-minded to recognize a common view is that the best simulations > and models are so much hand-waving until they are tested and validated by > experiment. Certainly as a modeler, my primary function is to design > experiments. So I darn well better understand the limitations of the > experimental techniques and materials available to the wet-lab people, their > motivations, etc., etc. Well, this is an other can of worms. There is no such thing as a purely experimental science. Even when you peer through a microscope, you trust the theory of optics to evaluate what you see. When you use synchrotron radiation to deduce the structure of a protein, the amount of theory (even simulation!) that goes in between the reading on the detectors and the final structure is pretty large. So I don't think it is useful to claim the upper hand for either theory or experiment - they are both indispensable for progress in Science. As for this 'talking' business: naturally, we are not discussing social skills. By being able to talk to an 'experimentalist' (myself being a computational chemist) I mean that I would/should be able to understand the capabilities, limitations of their results. What I would expect from the experimentalists who wants to talk to me is that they understand what my calculations can contribute and what our limitations are. I have seen both unwarranted ridicule of and uwarranted trust in computational results - neither are beneficial to progress. Mihaly Mezei, Dept. of Physiology & Biophysics, Mount Sinai School of Medicine Voice: (212) 241-2186 Fax: (212) 860-3369| WWW (MSSM home): http:// adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei From chemistry-request@server.ccl.net Tue Nov 12 16:52:50 2002 Received: from web21006.mail.yahoo.com ([216.136.227.60]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gACLqoQ19341 for ; Tue, 12 Nov 2002 16:52:50 -0500 Message-ID: <20021112215250.55129.qmail@web21006.mail.yahoo.com> Received: from [148.218.36.120] by web21006.mail.yahoo.com via HTTP; Tue, 12 Nov 2002 13:52:50 PST Date: Tue, 12 Nov 2002 13:52:50 -0800 (PST) From: Cesar Millan Subject: CHARMM installation on IBMRS/6000 To: charmm-bbs@csir.org Cc: CHEMISTRY@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi! Someone knows How to install CHARMM28 on IBMPRS/6000. The parallel.doc doesn't mention nothing about it. thank you. -- Cesar Millan P. Facultad de Ciencias. Universidad Autonoma del Estado de Morelos __________________________________________________ Do you Yahoo!? U2 on LAUNCH - Exclusive greatest hits videos http://launch.yahoo.com/u2 From chemistry-request@server.ccl.net Tue Nov 12 13:41:23 2002 Received: from net.bluemoon.net ([63.237.147.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gACIfNQ14680 for ; Tue, 12 Nov 2002 13:41:23 -0500 Received: from localhost (fantom@localhost) by net.bluemoon.net (8.12.4/8.12.4) with ESMTP id gACIfHLI020169; Tue, 12 Nov 2002 13:41:17 -0500 (EST) (mail-from fant@pobox.com) X-Authentication-Warning: net.bluemoon.net: fantom owned process doing -bs Date: Tue, 12 Nov 2002 13:41:17 -0500 (EST) From: Andrew Fant X-X-Sender: fantom@net.bluemoon.net To: Surjit Dixit cc: "chemistry@ccl.net" Subject: Re: CCL:whom to teach what In-Reply-To: <3DD13011.2050607@wesleyan.edu> Message-ID: <20021112132748.Y18513-100000@net.bluemoon.net> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII At the risk of dredging up unpleasant memories from Grad School, I was told that this is why grad students are required to go to departmental seminars. As someone who was working with ab inito computations on 4-6 heavy atom systems in a group with no experimental work being done, I asked why I was required to stop this work, and go hear the latest on some strange synthetic pathway or electroanalytical technique. My advisor made a strong case when he said that it was to ensure that I could talk to people who weren't experts in my specialty, and to develop the knack for asking questions that might find common ground. Andy Andrew Fant | This | "If I could walk THAT way... Molecular Geek | Space | I wouldn't need the talcum powder!" fant@pobox.com | For | G. Marx (apropos of Aerosmith) Boston, MA USA | Hire | http://www.pharmawulf.com On Tue, 12 Nov 2002, Surjit Dixit wrote: > I am not sure if we are taught anywhere about "how to talk to a > 'scientist from such and such a field'". I guess the > talent to "talk" is something each individual develops to different > degree depending on their own interest and > approach to the problem at hand. > We were watching the dramatised version of the times before the > discovery of DNA structure in the film > "The Race to the Double Helix" yesterday. The Watson and Crick > achievment was greatly driven by their ability > to "talk", grasp and appreciate all the various bits of information > about DNA that was floating around in the various > communities. Whosoever may do the talking, the result is good for science. > The need to talk is crucial for researchers in any field if they wish to > answer the "big" questions and get the usefulness > of their work appreciated by the other community. This becomes > especially true for the computational chemist, since > our field is the new-comer and is demanding the recognition. > Surjit From chemistry-request@server.ccl.net Tue Nov 12 15:15:16 2002 Received: from web20603.mail.yahoo.com ([216.136.226.161]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gACKFGQ16698 for ; Tue, 12 Nov 2002 15:15:16 -0500 Message-ID: <20021112201516.48154.qmail@web20603.mail.yahoo.com> Received: from [206.111.112.115] by web20603.mail.yahoo.com via HTTP; Tue, 12 Nov 2002 12:15:16 PST Date: Tue, 12 Nov 2002 12:15:16 -0800 (PST) From: Sengen Sun Subject: Re: CCL:a bit more on molecular computational chemistry To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I personally think that computational chemistry should be attached to specific chemical disciplines. In that way, the scientific concepts in a corresponding field can be well respected, and we can maintain the integrity of the physical sciences. As I discussed in my 3 preprint papers (http://www.ccl.net/cgi-bin/ccl/message.cgi?2002+10+19+003), there have been some mistakes in pursuing an independence of computational chemistry for the last decades. For example, there has been a trend that chemical events are “explained” merely by some numbers or signs generated by the computational processes, while the meanings of the numbers and signs are not clear in the corresponding scientific discipline or in the physical reality. When I read Fukui’s Nobel lecture (http://www.nobel.se/chemistry/laureates/1981/fukui-lecture.html, also published in Science and Angew. Chem. Int. Ed.), I was even confused by what the scientific definition of “potential energy” is. His lecture implies to me the potential energy is about the stabilization and destabilization of the orbitals. After solving the S-equation, some existing mechanistic theories were rejected by creating a new “theory”. I doubt that a process of solving a mathematical equation can create a new “scientific” theory without going back to the physical reality in that particular discipline. Just my personal opinions. Sengen __________________________________________________ Do you Yahoo!? U2 on LAUNCH - Exclusive greatest hits videos http://launch.yahoo.com/u2