From chemistry-request@server.ccl.net Fri Oct 15 00:06:34 1999 Received: from tucc-exchange.trinity.edu (Tucc15.Tucc.Trinity.Edu [131.194.151.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA24175 for ; Fri, 15 Oct 1999 00:06:33 -0400 Received: by Tucc15.Tucc.Trinity.Edu with Internet Mail Service (5.5.2448.0) id <4JM9PZ87>; Thu, 14 Oct 1999 22:57:03 -0500 Message-ID: From: "Mills, Nancy S." To: chemistry@ccl.net Subject: Use of DFT in calculations of NICS Date: Thu, 14 Oct 1999 22:57:03 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" I am calculating nucleus independent chemical shifts (NICS) for a fluorenyl cation with a positively charged substituent at the 9-position. I am examining the effect of rotation around the bond between the substituent and the fluorenyl ring. Calculations with RHF/6-31g* give reasonable results ( the maximum difference between values for the five-membered ring is about a factor of two) , but with B3LYP/6-31g*, the NICS values vary between 28 and 390 for the five-membered ring. Note: exactly the same set of geometries is used for the RHF/6-31G(d) and B3LYP/6-31G(d) calculations of NICS. Also, when we have compared the calculated NMR shift of these kind of dications with the experimental values, calculations with B3LYP/6-31g(d) are a bit better than those with RHF/6-31G(d). Is there a reason why calculations with B3LYP to get NICS would vary so much with the twisting of a substituent? Thanks. Nancy Mills Phone, (210) 999-7317 Professor and Chair Fax, (210) 999-7317 Department of Chemistry nmills@trinity.edu Trinity University 715 Stadium Dr. San Antonio, TX 78212-7200 From chemistry-request@server.ccl.net Fri Oct 15 03:35:05 1999 Received: from hydra.chem.rug.nl (hydra.chem.rug.nl [129.125.35.229]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA25054 for ; Fri, 15 Oct 1999 03:35:04 -0400 Received: from [129.125.7.13] (theochem1.chem.rug.nl [129.125.7.13]) by hydra.chem.rug.nl (AIX4.2/UCB 8.7/8.7) with ESMTP id JAA23734 for ; Fri, 15 Oct 1999 09:47:55 +0200 (MET DST) X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 15 Oct 1999 09:30:07 +0200 To: CHEMISTRY@ccl.net From: Marcel Swart Subject: Re: CCL:Q: greek letters in HTML? I really love it when people are so conservatively convinced about some computer program .. It is almost like religion. The answer should of course have been: it depends on which version of HTML you are referring to, since in HTML 4.0 there are some new features regarding this. The fastest way is however, to put a FONT tag around the text: a for an alpha, etc. >latex2html --- > >everything should be done in tex/latex...just for your reference. >iraj. > >Iraj Daizadeh, Ph.D. >Email: daizadeh@nucleus.harvard.edu > >On Fri, 15 Oct 1999, Kieran F Lim (Lim Pak Kwan) wrote: > >> How can I put greek letters into a HTML page? >> Can someone please point me to a reference/help site? >> >> thanks >> >> Kieran >> ------------------------------------------------------------ >> Dr Kieran F Lim Biol. and Chemical Sciences >> (Lim Pak Kwan) Deakin University >> ph: + [61] (3) 5227-2146 Geelong VIC 3217 >> fax: + [61] (3) 5227-1040 AUSTRALIA >> mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim ========================================= drs. Marcel Swart Theoretical Chemistry (MSC) Molecular Dynamics (GBB) Rijksuniversiteit Groningen Chemistry Department Nijenborgh 4 9747 AG Groningen The Netherlands tel : +31 - (0)50 - 3634377 fax : +31 - (0)50 - 3634441 E-mail : m.swart@chem.rug.nl WWW: http://hydra.chem.rug.nl/~swart/ ========================================= From chemistry-request@server.ccl.net Fri Oct 15 03:48:35 1999 Received: from isis.och.bme.hu (root@isis.szk.bme.hu [152.66.61.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA25140 for ; Fri, 15 Oct 1999 03:48:33 -0400 Received: from web.inc.bme.hu (pii.inc.bme.hu [152.66.63.31]) by isis.och.bme.hu (8.9.3/8.9.3) with ESMTP id JAA15317; Fri, 15 Oct 1999 09:42:05 +0200 Message-ID: <3806D8F4.325E32D9@web.inc.bme.hu> Date: Fri, 15 Oct 1999 09:34:12 +0200 From: csonka X-Mailer: Mozilla 4.61 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: Lou Noodleman CC: yubofan@guomai.sh.cn, chemistry@ccl.net Subject: Re: CCL:Why aren't DFT methods suitable for long distance interactions? References: <199910141916.MAA11093@degas.scripps.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Yubo Fan and CCL readers, I agree with the opinion of Lou Noodleman. DFT in the form of gradient corrected potentials (GGA) has proved suitable for many applications involving H-bonds. (LSDA is not suitable). I would like to add one probably important success of GGA-ACM-DFT: the description of OH...O interactions in sugar molecules. The following paper discusses some details: G.I. Csonka et al: Chem. Phys. Lett. 257 (1996) 49-60. futher references can be found on my home page. It is also true that that quite weak H-bonds are difficult for DFT. Weak long range Van der Waals interactions (dispersion energies) are missing from DFT. Walter Kohn was working on dispersion energies within DFT framework (DFT97, Wienna). Also John Perdew had some interesting papers about the long range interactions. Gabor I. Csonka Budapest University of Technology FAX: (361) 463.36.42 Inorganic Chemistry Dept. Ch. Bldg csonka@web.inc.bme.hu H-1111, Bp. Szent Gellert ter 4 http://web.inc.bme.hu/~csonka/csg.html http://www.ch.bme.hu/inc/csg.html From chemistry-request@server.ccl.net Fri Oct 15 03:49:00 1999 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA25152 for ; Fri, 15 Oct 1999 03:48:58 -0400 Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id KAA19259 for ; Fri, 15 Oct 1999 10:34:56 +0300 (EET DST) Date: Fri, 15 Oct 1999 10:34:52 +0300 (EET DST) From: John Kerkines To: chemistry@ccl.net Subject: Re: CCL:Q: greek letters in HTML? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 15 Oct 1999, Kieran F Lim (Lim Pak Kwan) wrote: > How can I put greek letters into a HTML page? > Can someone please point me to a reference/help site? > Hi Kieran, Check out a very useful page at http://www.hri.org/fonts/ There you'll find all the information you'll need for Greek Support in the most popular Windows applications, including Web Browsers. The official prototype for Greek characters in HTML pages is ISO-8859-7. If you want to WRITE greek in an html page, you must have a) greek fonts (available at many greek sites) b) in Windows, you can use Netscape Composer and use these greek fonts by changing the encoding to ISO-8859-7. Latin characters are not altered, but many accented latin letters (like the "o" in Schrodinger) will be shown as "?" in the page. I am not sure whether the newer HTML drafts support multi-language encoding in one page. If you have any questions please email me, Regards, John Kerkines Athens, Greece From chemistry-request@server.ccl.net Thu Oct 14 16:38:52 1999 Received: from wodc7-1.relay.mail.uu.net (wodc7-1.relay.mail.uu.net [199.171.54.114]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22000 for ; Thu, 14 Oct 1999 16:38:52 -0400 Received: from wodc7-1.uucp-gw.mail.uu.net by wodc7mr0.ffx.ops.us.uu.net with ESMTP (peer crosschecked as: wodc7-1.uucp-gw.mail.uu.net [199.171.54.178]) id QQhkyc11832; Thu, 14 Oct 1999 20:33:14 GMT Received: from wodc7uc0.ffx.ops.us.uu.net by wodc7ug0.ffx.ops.us.uu.net with SMTP (peer crosschecked as: wodc7-1.uucp.uu.net [199.171.54.179]) id QQhkyc12327; Thu, 14 Oct 1999 20:32:56 GMT Received: from m10.UUCP by wodc7uc0.ffx.ops.us.uu.net with UUCP/RMAIL ; Thu, 14 Oct 1999 20:32:56 +0000 Received: from gershwin by m10.gaussian.com; Thu, 14 Oct 1999 16:30:22 -0400 Received: (from ochtersk@localhost) by gershwin (980427.SGI.8.8.8/980728.SGI.AUTOCF) id QAA25930; Thu, 14 Oct 1999 16:28:49 -0400 (EDT) Date: Thu, 14 Oct 1999 16:28:49 -0400 From: Joe Ochterski To: Bernd Melchers Cc: chemistry@ccl.net Subject: Re: CCL:Installation of g98 Rev A7 Message-ID: <19991014162849.D25481@gershwin> Reply-To: gaussian.com!ochtersk@gaussian.com References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.4i In-Reply-To: ; from Bernd Melchers on Thu, Oct 14, 1999 at 04:18:10PM +0200 On Thu, Oct 14, 1999 at 04:18:10PM +0200, Bernd Melchers wrote: > 'Jens Antony wrote:' > > > > Dear all! > > > > We are installing the new version of Gaussian98 on an SGI R10000. The > > compilation finishes without obvious error messages. When executing the > > program, however, it stops without reading the input and writes a core > > You need a Makefile suitable for your compiler version. > Our gaussian98 A6 generates core dumps with compiler versions 7.3.1 (IRIX 6.5.5) > but not with compiler 7.2.x. There is a new Makefile available from > gaussian for 7.3.0 Compilers but it produces code which is > 30 % slower. And occasionally dumps core, also. > It seems, the people at gaussian have to do some further > developement. > > But who should be blamed for bad code, the compiler developer > at sgi or the programmer at gaussian??? > This answer is not only to Bernd, but is intended to clear up the confusion regarding compiling G98 with SGI compilers. Gaussian 98 Rev A.7 is currently certified with two SGI compilers: 1) 7.2.1 with patch3265. This is a compiler patch, so once you get the patch you must recompile. The patch is required to fully support the use of 64 bit integers throughout the program. Using 64 bit integers removes the 16Gb file size limit in previous releases of Gaussian. It also effectively removes any memory size limitation. 2) 7.3.0 with the new sgi.make file, which is available from help@gaussian.com. Rev A.7 was released before the 7.3 compilers were widely available, so we needed to update the makefile after A.7 was released. We are not aware of any general performance problem associated with the 7.3 compilers, or with the makefile we use for those compilers. I will be more than happy to look into any such problems. Just send them along to help@gaussian.com. The makefile for 7.3.1 has not been released yet. We are aware that certain jobs crash/get wrong answers when this compiler is used to build G98 Rev A.7. The 7.2, 7.1 and earlier compilers have not been fully certified. In general it is not safe to revert to "old" makefiles. Frequently, there are changes which turn down optimization on subroutines which we've discovered cause problems. The current makefile will also have the appropriate flags for compiling code added since the earlier release. Nor is it "safe" to use older compilers for the current release of Gaussian. By default, Gaussian uses the highest level of compiler optimization. New code in Gaussian can trip up older compilers, sometimes without the user being aware of it. Using the wrong makefile or an uncertified compiler can cause crashes, and perhaps worse than that, lead to incorrect results. You can find the compiler and OS requirements for the latest release of Gaussian at http://www.gaussian.com/g98_req.htm Generally, technical questions about Gaussian can be addressed to help@gaussian.com. We try very hard to answer all questions quickly and accurately. -- Joseph Ochterski, Ph.D Senior Customer Service Scientist help@gaussian.com From chemistry-request@server.ccl.net Fri Oct 15 01:30:53 1999 Received: from lh2.rdc1.sdca.home.com (ioracle@ha2.rdc1.sdca.home.com [24.0.3.67]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA24522 for ; Fri, 15 Oct 1999 01:30:53 -0400 Received: from home.com ([24.5.251.87]) by lh2.rdc1.sdca.home.com (InterMail v4.01.01.00 201-229-111) with ESMTP id <19991015052502.CVEJ5567.lh2.rdc1.sdca.home.com@home.com>; Thu, 14 Oct 1999 22:25:02 -0700 Message-ID: <3806BAC0.1BE12348@home.com> Date: Thu, 14 Oct 1999 22:25:20 -0700 From: "TJ O'Donnell" Reply-To: tjo@acm.org X-Mailer: Mozilla 4.61 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: ccl , lim@deakin.edu.au Subject: greek letters in html Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit You can use HTML "character entities" such as α β γ and Α Β Γ etc. Most browsers will render these properly, but it you may have to use the tag as well. It is possible for users to override any you have specified. There is no way to absolutely guarantee the greek letters (or any character, actually) will be rendered as you intended it. As for a reference, I find the O'Reilly books excellent, for example "Dynamic HTML" by Danny Goodman has a table of character entities on page 1018. Try this link as well. http://www.w3.org/MarkUp/html3/mathsym.html TJ O'Donnell tjo@acm.org On Fri, 15 Oct 1999, Kieran F Lim (Lim Pak Kwan) wrote: > How can I put greek letters into a HTML page? > Can someone please point me to a reference/help site? From chemistry-request@server.ccl.net Fri Oct 15 04:12:19 1999 Received: from uni-paderborn.de (uni-paderborn.de [131.234.22.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA25491 for ; Fri, 15 Oct 1999 04:12:14 -0400 Received: from oc24 ([131.234.240.84]:1229 "EHLO uni-paderborn.de") by mail.uni-paderborn.de with ESMTP id ; Fri, 15 Oct 1999 10:06:09 +0200 Message-ID: <3806EE77.C8B67A6E@uni-paderborn.de> Date: Fri, 15 Oct 1999 10:05:59 +0100 From: Edgar X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: "Kieran F Lim (Lim Pak Kwan)" CC: chemistry@ccl.net Subject: Re: CCL:Q: greek letters in HTML? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The HTML 4.0 syntax like α doesn't work with actual Netscape browsers :-( (I don't know how the MSIE behaves), and the hint by Marcel is not doing well under Unix. There is no real solution (AFAIK) at the moment and therefore I can't give you one. =============================== Edgar Luttmann eMail: edgar@upb.de phone: (+49) 5251 60-4236 From chemistry-request@server.ccl.net Fri Oct 15 05:09:58 1999 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA25798 for ; Fri, 15 Oct 1999 05:09:58 -0400 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 11c3HB-0000ri-00; Fri, 15 Oct 1999 10:03:49 +0100 Received: from sg1.cc.ic.ac.uk ([155.198.63.8] helo=cscmgb.cc.ic.ac.uk) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 11c3Gh-0001Gq-00; Fri, 15 Oct 1999 10:03:19 +0100 Received: from [155.198.224.86] by cscmgb.cc.ic.ac.uk (980427.SGI.8.8.8/4.0) id KAA07652; Fri, 15 Oct 1999 10:03:18 +0100 (bst) Mime-Version: 1.0 X-Sender: rzepa@155.198.63.8 Message-Id: In-Reply-To: <3802213A.3D9D85EC@u.arizona.edu> References: <3802213A.3D9D85EC@u.arizona.edu> Date: Fri, 15 Oct 1999 10:03:11 +0100 To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: Re: CCL:Beowulf+Chemistry web site Cc: r.c.walker@ic.ac.uk, steve@serf.org, Brett Bode Content-Type: text/plain; charset="us-ascii" > > >I made some web pages for the talk. The site is definitely "under >construction". I'll try to work on the site since there seems to be some >interest. The theme is "Beowulf Clusters for Chemists". > >http://www.chem.arizona.edu/theochem/beowulf > >The promised summary of e-mail responses to my original posting is at > >http://www.chem.arizona.edu/theochem/beowulf/chemsites.html > Regarding parallel implementations of chemistry, has anyone heard of any chemical applications of the related "Appleseed Project" http://exodus.physics.ucla.edu/appleseed/appleseed.html The new G4 processor is much better at floating point than the G3, and it might even come close to Pentium systems (?). Certainly the SETI project reveals that for the FT (integer) type of operations, G3 processors "appear" to substantially outperform Pentiums. Henry Rzepa. +44 171 594 5774 (Office) +44 171 594 5804 (Fax) http://www.ch.ic.ac.uk/rzepa/ From chemistry-request@server.ccl.net Fri Oct 15 05:22:00 1999 Received: from tc11.theochem.uni-stuttgart.de (teomgs@tc11.theochem.uni-stuttgart.de [129.69.55.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA25942 for ; Fri, 15 Oct 1999 05:21:54 -0400 Received: from localhost (teomgs@localhost) by tc11.theochem.uni-stuttgart.de (8.8.6 (PHNE_13947)/8.8.6) with ESMTP id LAA29966; Fri, 15 Oct 1999 11:13:56 +0200 (MDT) X-Authentication-Warning: tc11.theochem.uni-stuttgart.de: teomgs owned process doing -bs Date: Fri, 15 Oct 1999 11:13:56 +0200 (MDT) From: "Dr. Martin Schuetz" To: csonka cc: Lou Noodleman , yubofan@guomai.sh.cn, chemistry@ccl.net Subject: Re: CCL:Why aren't DFT methods suitable for long distance interactions? In-Reply-To: <3806D8F4.325E32D9@web.inc.bme.hu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII One should be aware, that the dispersive contribution to a hydrogen bond of the type H2O-H2O is about 20 %, hence far from negligible. (this can e.g. be seen in SAPT or local correlation calculations). Therefore, one should be aware, that the relatively good agreement between GGA DFT methods and MP2 is fortuitious, i.e. a result of error cancellation. A good choice and reliable method for describing hydrogen bonded systems is MP2. ---------------------------------------------------------------------------- Dr. Martin G. Schuetz Phone: 0049 (0)711-685-4397 University of Stuttgart Fax: 0049 (0)711-685-4442 Institute for Theoretical Chemistry Pfaffenwaldring 55 Room Nr: 8.161 D-70569 Stuttgart Email: schuetz@theochem.uni-stuttgart.de WWW : http://www.theochem.uni-stuttgart.de/~teomgs/ ---------------------------------------------------------------------------- On Fri, 15 Oct 1999, csonka wrote: > Dear Yubo Fan and CCL readers, > > I agree with the opinion of Lou Noodleman. DFT in the form of gradient > corrected potentials (GGA) has > proved suitable for many applications involving H-bonds. (LSDA is not > suitable). > I would like to add one probably important success of GGA-ACM-DFT: the > description of OH...O interactions in sugar molecules. > The following paper discusses some details: > G.I. Csonka et al: Chem. Phys. Lett. 257 (1996) 49-60. > > futher references can be found on my home page. > > It is also true that that quite weak H-bonds are difficult for DFT. Weak > long range Van der Waals interactions > (dispersion energies) are missing from DFT. > > Walter Kohn was working on dispersion energies within DFT framework > (DFT97, Wienna). Also John Perdew had some interesting papers about the > long range interactions. > > Gabor I. Csonka Budapest University of Technology > FAX: (361) 463.36.42 Inorganic Chemistry Dept. Ch. Bldg > csonka@web.inc.bme.hu H-1111, Bp. Szent Gellert ter 4 > http://web.inc.bme.hu/~csonka/csg.html > http://www.ch.bme.hu/inc/csg.html > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Fri Oct 15 07:00:57 1999 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA27336 for ; Fri, 15 Oct 1999 07:00:50 -0400 Received: from p100 ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id SAA23658 for ; Fri, 15 Oct 1999 18:51:06 +0800 (CST) Message-Id: <199910151051.SAA23658@ms.dicp.ac.cn> Date: Fri, 15 Oct 1999 19:0:44 +0800 From: Li Guo Hui To: "CHEMISTRY@ccl.net" Subject: How can get charge distribution fastly and correctly in MDS of biomolecules. Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear,CCLERS: i am not very farmillar with Molecular Dynamics Simulation of macromolecule or biomolecules.i had a question about this. during the simulation, how can one get charge distribution of biomolecule correctly and fastly. i would summary reply for you. thanks in advance Best Wishes With You From chemistry-request@server.ccl.net Fri Oct 15 07:00:56 1999 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA27335 for ; Fri, 15 Oct 1999 07:00:49 -0400 Received: from p100 ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id SAA23654 for ; Fri, 15 Oct 1999 18:50:58 +0800 (CST) Message-Id: <199910151050.SAA23654@ms.dicp.ac.cn> Date: Fri, 15 Oct 1999 19:0:37 +0800 From: Li Guo Hui Reply-To: chenhua@ms.dicp.ac.cn To: "CHEMISTRY@ccl.net" Subject: How can get charge distribution fastly and correctly in MDS of biomolecules. Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear,CCLERS: i am not very farmillar with Molecular Dynamics Simulation of macromolecule or biomolecules.i had a question about this. during the simulation, how can one get charge distribution of biomolecule correctly and fastly. i would summary reply for you. thanks in advance Best Wishes With You From chemistry-request@server.ccl.net Fri Oct 15 09:46:02 1999 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA28454 for ; Fri, 15 Oct 1999 09:46:01 -0400 Received: from ccshst01 (wtian@ccshst01.cs.uoguelph.ca [131.104.96.81] (may be forged)) by ccshst09.cs.uoguelph.ca (8.8.6 (PHNE_17135)/8.8.6) with SMTP id JAA00798; Fri, 15 Oct 1999 09:38:17 -0400 (EDT) Date: Fri, 15 Oct 1999 09:38:15 -0400 (EDT) From: WeiQuan Tian X-Sender: wtian@ccshst01 To: "Dr. Martin Schuetz" cc: csonka , Lou Noodleman , yubofan@guomai.sh.cn, chemistry@ccl.net Subject: Re: CCL:Why aren't DFT methods suitable for long distance interactions? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There is a paper of Dr. Weitao Yang : J. Chem. Phys. 107(19), 7921-7925, 1997 for the analysis of GGA on van der Waals interaction. Actually in the normal case ( except the pure disperion interaction), there are charge transfer, static electric interaction and so on. Also, the performance of GGA on such interaction is individual. Wei Quan Tian On Fri, 15 Oct 1999, Dr. Martin Schuetz wrote: > One should be aware, that the dispersive contribution to a hydrogen bond > of the type H2O-H2O is about 20 %, hence far from negligible. (this can > e.g. be seen in SAPT or local correlation calculations). Therefore, one > should be aware, that the relatively good agreement between GGA DFT > methods and MP2 is fortuitious, i.e. a result of error cancellation. > A good choice and reliable method for describing hydrogen bonded systems > is MP2. > > > ---------------------------------------------------------------------------- > Dr. Martin G. Schuetz Phone: 0049 (0)711-685-4397 > University of Stuttgart Fax: 0049 (0)711-685-4442 > Institute for Theoretical Chemistry > Pfaffenwaldring 55 Room Nr: 8.161 > D-70569 Stuttgart > Email: schuetz@theochem.uni-stuttgart.de > WWW : http://www.theochem.uni-stuttgart.de/~teomgs/ > ---------------------------------------------------------------------------- > > > > On Fri, 15 Oct 1999, csonka wrote: > > > Dear Yubo Fan and CCL readers, > > > > I agree with the opinion of Lou Noodleman. DFT in the form of gradient > > corrected potentials (GGA) has > > proved suitable for many applications involving H-bonds. (LSDA is not > > suitable). > > I would like to add one probably important success of GGA-ACM-DFT: the > > description of OH...O interactions in sugar molecules. > > The following paper discusses some details: > > G.I. Csonka et al: Chem. Phys. Lett. 257 (1996) 49-60. > > > > futher references can be found on my home page. > > > > It is also true that that quite weak H-bonds are difficult for DFT. Weak > > long range Van der Waals interactions > > (dispersion energies) are missing from DFT. > > > > Walter Kohn was working on dispersion energies within DFT framework > > (DFT97, Wienna). Also John Perdew had some interesting papers about the > > long range interactions. > > > > Gabor I. Csonka Budapest University of Technology > > FAX: (361) 463.36.42 Inorganic Chemistry Dept. Ch. Bldg > > csonka@web.inc.bme.hu H-1111, Bp. Szent Gellert ter 4 > > http://web.inc.bme.hu/~csonka/csg.html > > http://www.ch.bme.hu/inc/csg.html > > > > > > > > > > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl..net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri Oct 15 10:03:45 1999 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA28604 for ; Fri, 15 Oct 1999 10:03:37 -0400 Received: from p100 ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id VAA24814; Fri, 15 Oct 1999 21:52:31 +0800 (CST) Message-Id: <199910151352.VAA24814@ms.dicp.ac.cn> Date: Fri, 15 Oct 1999 22:2:8 +0800 From: Li Guo Hui Reply-To: chenhua@ms.dicp.ac.cn To: Yongxing Liu CC: "CHEMISTRY@ccl.net" Subject: Re: Re: CCL:How can get charge distribution fastly and correctly in MDS of biomolecules. Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear,Mr.Liu: >from what you told me, i got that: in principle, one should calculate charge distribution in molecule for each time step during simulation. major reason is that one cannot do this job just because it cost time very much if calculating for all steps. another minor reason is that forcefield with polarizale isnot existing. Best Wishes With You Li Guo Hui State Key Lab of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences From chemistry-request@server.ccl.net Fri Oct 15 10:58:42 1999 Received: from mailgw.cc.uga.edu (mailgw.cc.uga.edu [128.192.1.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA28883 for ; Fri, 15 Oct 1999 10:58:42 -0400 Received: from archa7.cc.uga.edu (arch7.cc.uga.edu) by mailgw.cc.uga.edu (LSMTP for Windows NT v1.1b) with SMTP id <0.01377E03@mailgw.cc.uga.edu>; Fri, 15 Oct 1999 10:52:50 -0400 Received: from archa15.cc.uga.edu (arch15.cc.uga.edu [128.192.95.115]) by archa7.cc.uga.edu (8.9.1/8.9.1) with ESMTP id KAA37578 for ; Fri, 15 Oct 1999 10:41:38 -0400 Received: from localhost (dmoran@localhost) by archa15.cc.uga.edu (8.9.1/8.9.1) with ESMTP id KAA59192 for ; Fri, 15 Oct 1999 10:41:37 -0400 X-Authentication-Warning: archa15.cc.uga.edu: dmoran owned process doing -bs Date: Fri, 15 Oct 1999 10:41:37 -0400 (EDT) From: Damian Krone-Moran X-Sender: dmoran@archa15.cc.uga.edu To: CHEMISTRY@ccl.net Subject: G94e2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII G'day I am trying to compile G94e2 on a PPC Power 3 SP RS/6000. The compilation fails without building any of the links. The frist error message to appear in the build log is : >>>> cc -DIBM_RS6K -DUSE_SYSV -DUSE_I2 -DDEFMAXSHL=2500 -DDEFMAXATM=1000 -DD EFMAXNZ=1200 -DDEFNVDIM=257 -DDEFARCREC=1024 -DDEFLMAX=13 -DDEFN3MIN=10 -DDEFM AXOP=120 -DMERGE_LOOPS -DUSE_ESSL -DDUMMY_RTEOPT -DDUMMY_UNDER -DGAUSS_PAR -qph sinfo -O -c bsd/mdutil.c "bsd/mdutil.c", line 1473.40: 1506-099 (S) Unexpected argument. "bsd/mdutil.c", line 1570.33: 1506-099 (S) Unexpected argument. C Init - Phase Ends; 0.000/ 0.000 IL Gen - Phase Ends; 0.210/ 0.220 make: 1254-004 The error code from the last command is 1. Stop. ar rlv ../util.a mdutil.o rs6kdum.o ar: Creating an archive file ../util.a. ar: A file or directory in the path name does not exist. ar: 0707-117 The fopen system call failed on file mdutil.o. ar: A file or directory in the path name does not exist. ar: 0707-117 The fopen system call failed on file rs6kdum.o. a - mdutil.o a - rs6kdum.o else if ( 0 || 0 ) then rm mdutil.o <<<< Later in the compilation, the following error message appears and the build dies: >>>> ld -r util.a -o utila.o xlf -qextname -qphsinfo -qcharlen=32760 -NQ70000 -NT240000 -ND15000 -NQ80000 -qspill=1000 -qmaxmem=-1 -qnosave -qhalt=s -O3 -qhot -qcache=assoc=4:line=128:size=256:type=d -qarch=pwr2 -qtune=pwr2 -o gau-worker gau-worker.o util.a -lblas -lc -bmaxdata:0x40000000 ld: 0711-317 ERROR: Undefined symbol: .times_ ld: 0711-317 ERROR: Undefined symbol: .gauabt_ ld: 0711-317 ERROR: Undefined symbol: .ntrext1_ ld: 0711-317 ERROR: Undefined symbol: .ntrsiz_ ld: 0711-317 ERROR: Undefined symbol: .writwa_ ld: 0711-317 ERROR: Undefined symbol: .readwa_ ld: 0711-317 ERROR: Undefined symbol: .waitwa_ ld: 0711-317 ERROR: Undefined symbol: .openwa_ ld: 0711-317 ERROR: Undefined symbol: .ntrbks_ ld: 0711-317 ERROR: Undefined symbol: .closwa_ ld: 0711-317 ERROR: Undefined symbol: .unlink_ ld: 0711-317 ERROR: Undefined symbol: .gauexec_ ld: 0711-317 ERROR: Undefined symbol: .gfree_ ld: 0711-317 ERROR: Undefined symbol: .fixenv_ ld: 0711-317 ERROR: Undefined symbol: .galloc_ ld: 0711-317 ERROR: Undefined symbol: .gctime_ ld: 0711-317 ERROR: Undefined symbol: .getscm_ ld: 0711-317 ERROR: Undefined symbol: .dgemm_ ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information. make: 1254-004 The error code from the last command is 8. Stop. if ( -e gauopt ) rm -f gauopt ln -s g94opt gauopt <<<< If anyone can help with this problem I would be very appreciative. Thank you for your time. Damian ----------------------------------------------------------------- Damian Krone-Moran, P.v.R. Schleyer Research Group, Computational Chemistry Annex, Department of Chemistry, University of Georgia,GA, 30602 Ph(706)-542-7513 Fax(706)-542-7514 www.arches.uga.edu/~dmoran From chemistry-request@server.ccl.net Fri Oct 15 13:20:51 1999 Received: from gobble.peptor.co.il ([212.150.27.195]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA29516 for ; Fri, 15 Oct 1999 13:20:49 -0400 Received: (qmail 1032 invoked from network); 15 Oct 1999 17:14:54 -0000 Received: from unknown (HELO peptor.co.il) (192.168.10.179) by gobble.peptor.co.il with SMTP; 15 Oct 1999 17:14:54 -0000 Message-ID: <38076180.DD77D7FF@peptor.co.il> Date: Fri, 15 Oct 1999 19:16:49 +0200 From: ella X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: protein-derived drugs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I was wondering if anyone knows of a review or short of that a paper that describes how a drug structure was derived from a protein structure. I'm referring to the case where the drug serves as a mimic to a protein that is a substrate to a protein receptor. Thank you, E. Nadler From chemistry-request@server.ccl.net Fri Oct 15 06:23:09 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA26267 for ; Fri, 15 Oct 1999 06:23:09 -0400 Received: from redox.scripps.edu (redox.scripps.edu [137.131.240.50]) by relay1.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id DAA14245; Fri, 15 Oct 1999 03:15:14 -0700 (PDT) Received: from localhost by redox.scripps.edu (8.9.1/TSRI-2.8) with SMTP id DAA09621; Fri, 15 Oct 1999 03:15:12 -0700 (PDT) Date: Fri, 15 Oct 1999 03:15:12 -0700 (PDT) From: "Jesus M. Castagnetto" Sender: jesusmc@scripps.edu To: chemistry@ccl.net cc: lim@deakin.edu.au Subject: Re: CCL:greek letters in html In-Reply-To: <3806BAC0.1BE12348@home.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Appart from the spec docs at the W3C site (http://www.w3c.org/), one of the best sites for HTML help is: http://www.htmlhelp.org/ There you will see that the HTML 4.0 specs call for Greek entities in the DTD (Document Type Definition), but as most know, the recent browsers only implement the transitional DTD, so some entities are not supported. The way to assure that the greek letter will show up as such is to use inline images, this avoids the problem of assuming that the person viewing the page has the "Symbol" font installed, and also avoids using the (now) deprecated tag. In the web site mentioned above, there is a link to a collections of glyphs >from the Unicode organization: http://charts.unicode.org/Unicode.charts/normal/Unicode.html And the images for the Greek set are at the URL: http://charts.unicode.org/Unicode.charts/normal/U0370.html Hope this helps. On Fri, 15 Oct 1999, Kieran F Lim (Lim Pak Kwan) wrote: > How can I put greek letters into a HTML page? > Can someone please point me to a reference/help site? -- Jesus M. Castagnetto - "Ken Zen Ichi-nyo" Program Project: http://www.scripps.edu/research/metallo/ Metalloprotein DB: http://metallo.scripps.edu/ Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/ From chemistry-request@server.ccl.net Fri Oct 15 10:06:54 1999 Received: from hscmg02.hou.ucarb.com (hscmg02.hou.ucarb.com [144.68.4.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA28638 for ; Fri, 15 Oct 1999 10:06:51 -0400 Received: by hscmg02.hou.ucarb.com with Internet Mail Service (5.5.2448.0) id <4WH085WV>; Fri, 15 Oct 1999 08:06:00 -0500 Message-ID: <47F7EAA0389AD011840500805FEAB9C60376E391@sctms01.sct.ucarb.com> From: "Fulton CR (Charles)" To: "'Joe Ochterski'" Cc: chemistry@ccl.net, "Smith JA (Jack)" , "Froese RD (Robert)" Subject: RE: Installation of g98 Rev A7 Date: Fri, 15 Oct 1999 08:05:02 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Joe, Will using the 7.3 compilers with the new makefile also fix the newzmat program under irix? With 7.2.1+patch3265 it core dumps ever time I run it. We don't really have any other problems with our rev a7 g98, compiled with 7.2.1 & patch3265. I do have the new makefile though for 7.3, I just have not upgraded our compilers yet. And if i'm going to lose 30% with certified 7.3+new makefile then it wouldn't make since to do the upgrade. I could try it though and let you know the results. Do you have any such suggestions or "clearing up" concerning compiling g98 rev a7 under linux? (other than pgi+opt. blas libs) thanks alot for this note it did clear up some things concerning what is certified under irix. -charlie. > ---------- > From: Joe Ochterski[SMTP:gaussian.com!ochtersk@gaussian.com] > Sent: Thursday, October 14, 1999 4:28 PM > To: Bernd Melchers > Cc: chemistry@ccl.net > Subject: CCL:Installation of g98 Rev A7 > > On Thu, Oct 14, 1999 at 04:18:10PM +0200, Bernd Melchers wrote: > > 'Jens Antony wrote:' > > > > > > Dear all! > > > > > > We are installing the new version of Gaussian98 on an SGI R10000. The > > > compilation finishes without obvious error messages. When executing > the > > > program, however, it stops without reading the input and writes a core > > > > You need a Makefile suitable for your compiler version. > > Our gaussian98 A6 generates core dumps with compiler versions 7.3.1 > (IRIX 6.5.5) > > but not with compiler 7.2.x. There is a new Makefile available from > > gaussian for 7.3.0 Compilers but it produces code which is > > 30 % slower. And occasionally dumps core, also. > > It seems, the people at gaussian have to do some further > > developement. > > > > But who should be blamed for bad code, the compiler developer > > at sgi or the programmer at gaussian??? > > > > > This answer is not only to Bernd, but is intended to clear up the > confusion regarding compiling G98 with SGI compilers. > > > Gaussian 98 Rev A.7 is currently certified with two SGI compilers: > > 1) 7.2.1 with patch3265. This is a compiler patch, so once you get the > patch you must recompile. The patch is required to fully support the use > of 64 bit integers throughout the program. Using 64 bit integers removes > the 16Gb file size limit in previous releases of Gaussian. It also > effectively removes any memory size limitation. > > 2) 7.3.0 with the new sgi.make file, which is available from > help@gaussian.com. Rev A.7 was released before the 7.3 compilers were > widely available, so we needed to update the makefile after A.7 was > released. > > We are not aware of any general performance problem associated with the > 7.3 compilers, or with the makefile we use for those compilers. I will be > more than happy to look into any such problems. Just send them along to > help@gaussian.com. > > > The makefile for 7.3.1 has not been released yet. We are aware that > certain jobs crash/get wrong answers when this compiler is used to build > G98 Rev A.7. > > The 7.2, 7.1 and earlier compilers have not been fully certified. > > In general it is not safe to revert to "old" makefiles. Frequently, there > are changes which turn down optimization on subroutines which we've > discovered cause problems. The current makefile will also have the > appropriate flags for compiling code added since the earlier release. > > Nor is it "safe" to use older compilers for the current release of > Gaussian. By default, Gaussian uses the highest level of compiler > optimization. New code in Gaussian can trip up older compilers, sometimes > without the user being aware of it. > > Using the wrong makefile or an uncertified compiler can cause crashes, and > perhaps worse than that, lead to incorrect results. > > > You can find the compiler and OS requirements for the latest release of > Gaussian at > > http://www.gaussian.com/g98_req.htm > > > Generally, technical questions about Gaussian can be addressed to > help@gaussian.com. We try very hard to answer all questions quickly and > accurately. > > > -- > Joseph Ochterski, Ph.D > Senior Customer Service Scientist > help@gaussian.com > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri Oct 15 13:33:35 1999 Received: from bluejay.prod.itd.earthlink.net (bluejay.prod.itd.earthlink.net [207.217.120.108]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA29598 for ; Fri, 15 Oct 1999 13:33:35 -0400 Received: from lrz.uni-muenchen.de (1Cust252.tnt1.rancho-cucamonga.ca.da.uu.net [63.24.225.252]) by bluejay.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id KAA22976; Fri, 15 Oct 1999 10:27:40 -0700 (PDT) Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id KAA14859; Fri, 15 Oct 1999 10:24:13 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14343.25405.170977.895258@lrz.uni-muenchen.de> Date: Fri, 15 Oct 1999 10:24:13 -0700 (PDT) To: "Rzepa, Henry" Cc: CHEMISTRY@ccl.net, r.c.walker@ic.ac.uk, steve@serf.org, Brett Bode Subject: CCL:Beowulf+Chemistry web site In-Reply-To: References: <3802213A.3D9D85EC@u.arizona.edu> X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid Rzepa, Henry writes: > The new G4 processor is much better at floating point than the G3, > and it might even come close to Pentium systems (?). Certainly the SETI It does not simply come close, it beats Pentium III by a substantial margin. > project reveals that for the FT (integer) type of operations, G3 processors "appear" > to substantially outperform Pentiums. Unfortunately, Athlons (700 MHz AMD Athlon has just been released) is even faster than G4: http://www.amd.com/products/cpg/athlon/benchmarks/specfp.html From chemistry-request@server.ccl.net Fri Oct 15 15:10:15 1999 Received: from rzusuntk.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA30477 for ; Fri, 15 Oct 1999 15:10:15 -0400 Received: [from rzusgi.unizh.ch (chburger@rzusgif.unizh.ch [130.60.68.19]) by rzusuntk.unizh.ch (8.8.5/SMI-5.31) with ESMTP id VAA12002 for ; Fri, 15 Oct 1999 21:04:19 +0200 (MET DST)] From: "Dr. Peter Burger" Received: [(chburger@localhost) by rzusgi.unizh.ch (8.8.8/SMI-IRIX6.2/USAR_MAIL_V2) id VAA04904 for CHEMISTRY@ccl.net; Fri, 15 Oct 1999 21:04:18 +0200 (MDT)] Message-Id: <199910151904.VAA04904@rzusgi.unizh.ch> Subject: CCL:Beowulf+Chemistry web site To: CHEMISTRY@ccl.net Date: Fri, 15 Oct 1999 21:04:18 +0200 (MDT) Action: s X-Mailer: ELM [version 2.4 PL25 PGP2] Content-Type: text > Unfortunately, Athlons (700 MHz AMD Athlon has just been released) is > even faster than G4: What do you mean by unfortunately - it's nice that they are so fast!! Nevertheless has someone achieved to produce a handtuned dgemm version for the Athlon? Just like GOTO's dgemm version for the Alpha 21164? Dgemm on the Athlon is not too bad though - using Clint Whaley's excellent Atlas library one obtains 530-540 MFLOPs on a 500 MHz Athlon That's still far off of the potentially accessible 1 GFlop though. Peter ------------------------------------------------------------- Peter Burger Universitaet Zuerich chburger@aci.unizh.ch From chemistry-request@server.ccl.net Fri Oct 15 15:46:07 1999 Received: from pneumatic-tube.sgi.com (pneumatic-tube.sgi.com [204.94.214.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA30701 for ; Fri, 15 Oct 1999 15:46:07 -0400 Received: from nodin.corp.sgi.com (fddi-nodin.corp.sgi.com [198.29.75.193]) by pneumatic-tube.sgi.com (980327.SGI.8.8.8-aspam/980310.SGI-aspam) via ESMTP id MAA05365; Fri, 15 Oct 1999 12:40:19 -0700 (PDT) mail_from (omar@boston.sgi.com) Received: from sgibos.boston.sgi.com (sgibos.boston.sgi.com [169.238.32.4] (may be forged)) by nodin.corp.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id MAA48826; Fri, 15 Oct 1999 12:39:39 -0700 (PDT) Received: from arkham.boston.sgi.com (arkham.boston.sgi.com [169.238.35.21]) by sgibos.boston.sgi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id PAA22064; Fri, 15 Oct 1999 15:39:36 -0400 (EDT) Received: from localhost (omar@localhost) by arkham.boston.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id PAA08336; Fri, 15 Oct 1999 15:39:35 -0400 (EDT) Date: Fri, 15 Oct 1999 15:39:34 -0400 (EDT) From: Omar Stradella To: "Fulton CR (Charles)" cc: "'Joe Ochterski'" , chemistry@ccl.net, "Smith JA (Jack)" , "Froese RD (Robert)" Subject: Re: CCL:Installation of g98 Rev A7 In-Reply-To: <47F7EAA0389AD011840500805FEAB9C60376E391@sctms01.sct.ucarb.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 15 Oct 1999, Fulton CR (Charles) wrote: > Joe, > > Will using the 7.3 compilers with the new makefile also fix the newzmat > program under irix? With 7.2.1+patch3265 it core dumps ever time I run it. > We don't really have any other problems with our rev a7 g98, compiled with > 7.2.1 & patch3265. No, it's not related to the compiler version. Do "limit stacksize 80000" before executing newzmat. Omar. +---------------------------------------------------------------------+ Omar G. Stradella, Ph.D. SGI / Chemistry and Biology Applications Group One Cabot Road, Hudson, MA 01749, USA N 42 22'40" W 71 33'44" E-mail: omar@boston.sgi.com Phone: +1-978-567-2258 FAX: +1-978-562-4755 http://www.sgi.com/chembio http://reality.sgi.com/omar +-------- Ph-nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn -------+ From chemistry-request@server.ccl.net Fri Oct 15 15:25:19 1999 Received: from charon.chem.uga.edu (karl@charon.chem.uga.edu [128.192.2.164]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA30562 for ; Fri, 15 Oct 1999 15:25:19 -0400 Received: from localhost (karl@localhost) by charon.chem.uga.edu (8.9.1/8.9.1) with ESMTP id PAA12779 for ; Fri, 15 Oct 1999 15:16:18 -0400 Date: Fri, 15 Oct 1999 15:16:18 -0400 (EDT) From: karl@ccmsd.chem.uga.edu To: CHEMISTRY@ccl.net Subject: Re: CCL:Why aren't DFT methods suitable for long distance interactions? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers To add to the conversation about DFT and long distant interaction I thought I may give and example. Recently, we did calculations on metal-rare gas dimers using HF, B3LYP, and MP2 thoeries implementing a large basis set. On the neutral dimers, which are bound by dispersion forces, HF and B3LYP did not locate bound states as where the MP2 calculations were able to do so. As the electrostatic contribution to the dimerization energy increased, by removing the metal's valence electrons, HF theory was able to locate bound states. B3LYP also located bound states but only after the electrostatic contibution became relatively larger. HF theory underestimated the binding of the charged dimers, as expected since HF theory does not include dispersion forces. B3LYP, which should follow a similar trend as HF, actually overestimated the binding energy relative to the MP2 values. The result of these calculation are presented in a paper which is about to be sent out for peer review in J. Chem. Phys.. For calculations, getting the right answer for the right reason is difficult to do. As pointed out earlier, often the good agreement with experiments are done due to fortuitous cancellations of error. The right reasons include convergence of all component to the dimerization energy (ie. dispersion, electrostatic, etc.) basis set convergence, valence versus valence plus core electron correlation, and BSSE (to correct for or not to correct for...) to name a few. To understand the approximations in the method is to understand the validity of the results. An excellent book on Hydrogen bonding that disscusses much of these issues: 1) S. Scheiner, Hydrogen Bonding, A Theoretical Perspective, Oxford University Press, 1997. Some papers relevant to DFT calculations of dispersion forces: 1) S. Kristyn and P. Pulay, Chem. Phys. Lett. 229, 175 (1994). 2) J. M. Perez-Jorda and A. D. Becke, Chem. Phys. Lett. 233, 134 (1995). 3) P. Hobza, J. Sponer and T. Reschel, J. Comput. Chem. 16, 1315 (1995). 4) D. C. Patton and M. R. Pederson, Int. J. Quantum Chem. 69, 619 (1998). 5) J. M. Prez-Jord, E. San-Fabin and A. J. Prez-Jimnez, J. Chem. Phys. 110, 1916 (1999). A paper for MP2 and dispersion (Ar2 dimer): 1) D. E. Woon, Chem. Phys. Lett 204, 29 (1993). Hope this adds constructively to the conversation. Sincerely, Karl _______________________________________________________________________________ | Karl Nicholas Kirschner |e-mail: karl@charon.chem.uga.edu Computational Center for |web: http://charon.chem.uga.edu/~karl Molecular Structure and Design |"...Experience is not what happens to a University of Georgia - Athens |man. Experience is what a man does with |what happens to him." Knox ___________________________________|___________________________________________ From chemistry-request@server.ccl.net Fri Oct 15 21:05:50 1999 Received: from nki001.netkonnect.net (nki001.netkonnect.net [208.198.32.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA31953 for ; Fri, 15 Oct 1999 21:05:50 -0400 Received: from netkonnect.net (rem33185.netkonnect.net [208.198.33.185]) by nki001.netkonnect.net (8.8.8/SCO5) with ESMTP id VAA04861; Fri, 15 Oct 1999 21:10:54 -0400 (EDT) Message-ID: <3807DDE8.F8F4C25C@netkonnect.net> Date: Fri, 15 Oct 1999 21:07:38 -0500 From: sherif X-Mailer: Mozilla 4.51 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "Dr. Moe Krauss" , lou@scripps.edu, yubofan@guomai.sh.cn, chemistry@ccl.net, "shaw@aro-emh1.army.mil" , "blaisten@cluster2.gmu.edu" , "cachau@ncifcrf.gov" , "carb@carb.nist.gov" , "carlos.gonzalez@nist.gov" , "guscus@katzo.rice.edu" , "jeffrey.hudgens@nist.gov" , "jerzy@kyoko.chem.fsu.edu" , "jl3@psu.edu" , "karl.irikura@nist.gov" , "kertesz@guvax.georgetown.edu" , "morokuma@emory.edu" , Nohad Gresh , "Professor Sokalski, Andrez" , "tcundari@mocha.memphis.edu" , "topol@ncifcrf.gov" , "walter.stevens@nist.gov" , "wing.tsang@nist.gov" , "rick@ncifcrf.gov" , "richard.kayser@nist.gov" Subject: Why aren't DFT methods suitable for long distance interactions?] X-Priority: 1 (Highest) References: <38072BCC.6B018B27@octank.carb.nist.gov> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Moe and colleagues: Thank you very much for the forwarded e-mail. I am glad that other scientists are beginning to question the validity of gradient correction for correlation in DFT. As you can see from my most recent J. Phys. Chem. Paper (Kafafi, S.A. vol 102(50), pp. 10404-10413, 1998), I have technically examined all of the available DFT methods (BLYP, B3LYP, B3WP91, BWP and Barrone's version PWPW...) which use gradient corrections for both exchange and correlation. I also wrote a small code which evaluates the gradient corrections for exchange and correlation separately. Upon performing the computations on weak van der Waal's systems I found that the gradient correction for exchange lowers the total energy, as one would expect from a HF point of view. However, the gradient correction for correlation changes sign for van der Waals systems and wipes out the lowering of the energy gained from exchange. This results in an overall repulsive interaction for van der Waal's systems. This was the true motivation for formulating the K2-BVWN method using gradient correction for exchange only. I could not state the above in the J. Phys. Chem. paper because this could lead to a war with other leading scientists that I knew I will not win. Furthermore, you may also notice that when I wrote the expression for Ec (equation 6 in the paper) I wanted a result at long range, r ---> oo, that will mimic the dispersion correlation (an attractive inverse sixth power dependence term). So, the only way to get this results was to move the GGA expression for exchange only with a different sign to the correlation expression. Accordingly, at r ---> oo, the first two-terms of equation 6 will decay exponentially to zero and the last GGA term will have the required negative sign and a weak inverse sixth power dependence. Again, I was very much silent in the paper to say the above bluntly because it may upset many leading scientists. I simply stated the results. This point becomes clear because the K2-BVWN method accounted for weak van der Waal's interactions in noble gases very well, while all of the other DFT methods predicted strongly repulsive interactions. Professor N. Handy in England stated to me that the K2-BVWN method gives quite impressive results, however, he still cannot understand why this is the case. In my opinion, Professor Handy is just using the gradient correction for correlation in exactly the same way as the B3LYP, BLYP, Barrone's PWPW etc. were formulated. ****** Gradient Corrections for Correlation are not needed in DFT ****** When we were in Poland last July, Professors Hobza and Gordon spent two-days in a row examining the math and the results in my J. Phys. Chem. paper. After numerous discussions with them, they were convinced that what I did was the correct approach to remedy the lack of proper dispersion interactions in DFT methods such as BLYP, B3LYP etc... I hope that the above cleared some of your doubts about the validity of the K2-BVWN approach. Please feel free to e-mail me if you have any questions. Very truly yours, Sherif Kafafi, CEO Density Functional Technologies Inc. "Dr. Moe Krauss" wrote: > -------- Original Message -------- > Subject: CCL:Why aren't DFT methods suitable for long distance > interactions? > Date: Thu, 14 Oct 1999 12:16:02 -0700 (PDT) > From: Lou Noodleman > To: yubofan@guomai.sh.cn > CC: chemistry@ccl.net > > Dear Yubo Fan and CCL, > DFT, especially in the form of gradient corrected potentials has > proved suitable for many applications involving H-bonds. This includes > water clusters, H-bond donor-acceptor systems, for metal ions in > solution (redox processes)(see Li et al Inorg. Chem. 1996, 35, > 4694-4702), > and for transition > metal complexes in proteins (metalloproteins)(Li et al., Inorg. chem. > 1999, 38,929-939, Konecny et al., Inorg. Chem. 1999, 38, 940-950). > Overall, fairly polar, > dipolar, or especially charged H bonds look to be well-represented in > most > cases. One Ref. is Pudzianowski, J.Phys.Chem.1996, 100, 4781-4789. > Another > example is the recent discussion and controversy in the literature over > low-barrier hydrogen bonds (LBHB) or more generally, short strong > hydrogen > bonds (SSHB). Hydrogen bond energies are quite similar for density > functional > (BLYP) versus ab initio MP2 results (for substituted formate-formic acid > dimers) > (see Kumar and McAlister J.A.C.S. 1998, 120, 3159). Whatever the outcome > of > this controversy, DFT methods look suitable for analyzing these issues. > DFT does have > some specific deficiencies for delocalized 3-electron bonds, which are > too > stable. So, for example, the ground state of the [(H2O)2]+ radical > cation is > incorrectly found as the "hemibond" structure rather than the correct > proton > transferred OH-H3O+ isomer.(Sodupe et al., J.Phys.Chem.A 1999, 103, > 166-170.) > This corresponds to a problem that my coworkers and I identified in DFT > long ago > (Noodleman, Post, Baerends Chem. Phys. 1982, 64, 159. This can be > partially > remedied by looking for broken symmetry DFT solutions with charge > asymmetry.) > Overall, however, this > is an atypical problem. In terms of H-bonded systems, it appears that > quite weak H-bonds are difficult for DFT. Weak long range Van der Waals > interactions > (dispersion energies) are also evidently not well treated by standard > DFT > methods from what I have seen (as might be expected). > Louis Noodleman > Department of Molecular Biology > The Scripps Research Institute, TPC15 > La Jolla, CA 92037 > >. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: > gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > Sherif: > > What do think of this? The GGA for the exchange is necessary but not the > correlation? Is that what your method proposes? > > Mo From chemistry-request@server.ccl.net Fri Oct 15 15:47:11 1999 Received: from mail.sciosinc.com (mail.sciosinc.com [199.89.163.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA30706 for ; Fri, 15 Oct 1999 15:47:04 -0400 From: zheng@sciosinc.com Received: by mail.sciosinc.com(Lotus SMTP MTA Internal build v4.6.2 (651.2 6-10-1998)) id 8825680B.006B7B19 ; Fri, 15 Oct 1999 12:33:58 -0700 X-Lotus-FromDomain: SCIOS To: chemistry@ccl.net Message-ID: <8825680B.006B7A0D.00@mail.sciosinc.com> Date: Fri, 15 Oct 1999 12:39:42 -0700 Subject: Calculation of LogP, logD, pKa and solubility Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Hi, I am looking for softwares for calculating physical and chemical properties of small molecules, including logP, logD, pKa, solubility, and etc. Specifically, I need executable programs that can read in, e.g. an SD file of 1 or more molecules, and then write out their corresponding calculated properties to an output file. I need to directly access the executable programs from within my own programs written in C++/Java without using any user-interface. While the ACD Labs in Toronto provides softwares to calculate logP, logD, pKa, and etc., it is not apparent whether and how these softwares can be accessed directly from a user's own programs. ACD softwares are rather expensive, e.g. the logP module is $3,900 whereas the logD module is $19,900, albeit such modules come with a lot bells and whistles that I don't really need. Any suggestions? Thanks, Qiang Zheng Sr. Scientist, PhD Scios Inc. 820 West Maude Avenue Sunnyvale, CA 94086 408-616-8253 (tel) 408-616-8206 (fax) zheng@sciosinc.com