From chemistry-request@ccl.net Wed Sep 3 02:41:37 2003 Received: from ciao.cc.columbia.edu (ciao.cc.columbia.edu [128.59.59.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h836faqG019707 for ; Wed, 3 Sep 2003 02:41:36 -0400 Received: from ciao.cc.columbia.edu (localhost [127.0.0.1]) by ciao.cc.columbia.edu (8.12.8/8.12.8) with ESMTP id h836fZdL009808 for ; Wed, 3 Sep 2003 02:41:36 -0400 (EDT) Received: from localhost by ciao.cc.columbia.edu (8.12.8/8.12.8/Submit) with ESMTP id h836fZ1c009805 for ; Wed, 3 Sep 2003 02:41:35 -0400 (EDT) X-Authentication-Warning: ciao.cc.columbia.edu: ak2048 owned process doing -bs Date: Wed, 3 Sep 2003 02:41:35 -0400 (EDT) From: Anil Korkut Sender: ak2048/at/columbia.edu To: chemistry/at/ccl.net Subject: Normal mode calculation with TINKER Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I like to make a normal mode analysis of a protein molecule with 4800 atoms (including hydrogens) using TINKER and I have two questions 1-I was able to minimize the structure to a gradient of 0.0000 using the truncated newton method and Amber96 parameters. Do you think this is enough to get non-negative eigenvectors? 2-I am trying to increase the maxvib to 15000 and MAxhess to 2000000 in sizes.i file but when I do so, the vibrate.f code can not be compiled due to memory limitations on my PC. what should be the minimum memory in order to compile the vibrate.f while the MAxvib=15000 Maxhess=2000000 thanks Anil Korkut From chemistry-request@ccl.net Wed Sep 3 08:31:15 2003 Received: from smtp2.ruc.dk (smtp2.ruc.dk [130.225.220.70]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h83CVEqG031961 for ; Wed, 3 Sep 2003 08:31:14 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 7905D1106856; Wed, 3 Sep 2003 14:31:13 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 547C01106852; Wed, 3 Sep 2003 14:31:12 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 3 Sep 03 14:31:12 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 3 Sep 03 14:31:04 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Piero Ugliengo , "Computational Chemistry List" Date: Wed, 3 Sep 2003 14:30:42 +0200 Subject: Re: CCL:IR intensity conversion factor Reply-To: spanget*at*ruc.dk Message-ID: <3F55FB1A.16128.A316772@localhost> Priority: normal In-reply-to: <3F4F12D9.8030405*at*unito.it> X-mailer: Pegasus Mail for Windows (v4.01) X-Spam-Status: No, hits=-0.5 required=5.0 tests=IN_REP_TO version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Piero Ugliengo: > I would like to know the exact formula that Gaussian98 is > using to convert the square of derivative of the > dipole moment with respect to a displacement > into the IR intensity in KM/mol. Dear Piero, you will find a general discussion of the problem, with references to the literature, in this paper (particularly page 715): B. A. Hess, Jr., L. J. Schaad, P. Carsky, R. Zahradnik, Chem. Rev. 86, 709-730 (1986) Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget*at*ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Wed Sep 3 09:01:51 2003 Received: from ds20.mpi-muelheim.mpg.de (ds20e.mpi-muelheim.mpg.de [192.108.70.44]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h83D1oqG001030 for ; Wed, 3 Sep 2003 09:01:50 -0400 Received: from pctritux.mpi-muelheim.mpg.de (pctritux.mpi-muelheim.mpg.de [172.17.104.6]) by ds20.mpi-muelheim.mpg.de (8.12.9/8.12.8) with ESMTP id h83D1XWB037033 for ; Wed, 3 Sep 2003 15:01:34 +0200 (MEST) From: Rolf Trinoga Reply-To: trinoga..at..mpi-muelheim.mpg.de Organization: Max-Planck-Institut fuer Strahlenchemie To: chemistry..at..ccl.net Subject: error compiling g03 on RedHat 8.0 with pgi v5.02 Date: Wed, 3 Sep 2003 15:01:03 +0200 User-Agent: KMail/1.5 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200309031501.04002.trinoga..at..mpi-muelheim.mpg.de> Hi, after upgrading to the Portland Group Compiler V5.02 on a RedHat 8.0 system it is not possible to compile g03 rev B01. [root@icmaster g03]# uname -a Linux icmaster 2.4.18-14custom #2 SMP Wed May 28 17:59:11 CEST 2003 i686 i686 i386 GNU/Linux First the location of the compiler and libs changed to: $(PGI)/linux86/5.0/ I corrected this: cd bsd vi bldg03 Changes in bldg03: # else if (-e $PGI/linux86/bin/pgf77) then else if (-e $PGI/linux86i/5.0/bin/pgf77) then vi i386.make Changes in i386.make: #PGILIBSL = $(PGI)/linux86/lib/libpgthread.so $(PGI)/linux86/lib/libpgc.so $(PGI)/linux86/lib/libpgftnrtl.a PGILIBSL = $(PGI)/linux86/5.0/lib/libpgthread.so $(PGI)/linux86/5.0/lib/libpgc.so $(PGI)/linux86/5.0/lib/libpgftnrtl.a [root@icmaster bsd]# cd .. [root@icmaster g03]# chmod +x bsd/install [root@icmaster g03]# bsd/install [root@icmaster g03]# bsd/bldg03 >& bldg03.log& [1] 2109 [root@icmaster g03]# The compilation stops with this error: Error while building g03: make[1]: Leaving directory `/opt/g03' pgf77 -mp -O2 -tp p7 -Mreentrant -Mrecursive -Mnosave -Minfo -Mneginfo -time -fast -Munroll -Mvect=assoc,recog,cachesize:524288,prefetch,sse -fastsse -Mscalarsse -o l202.exe ml202.o l202.a util.so -lm -lc l202.a(prtsgop.o): In function `prtsgop_': prtsgop.o(.text+0xa4): undefined reference to `irtyp_' l202.a(bldgen.o): In function `bldgen_': bldgen.o(.text+0x38): undefined reference to `iseat1_' make: *** [l202.exe] Error 2 if ( -e flc ) then endif How can I correct this? Thank you very much in advance. Best wishes, Rolf Trinoga Max-Planck-Institut fuer Bioanorganische Chemie Stiftstr. 34-36 D-45470 Muelheim a.d. Ruhr Germany From chemistry-request@ccl.net Wed Sep 3 09:05:29 2003 Received: from main.shu-bg.net (main.shu-bg.net [62.176.80.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h83D4hqG001219 for >ccl.net>; Wed, 3 Sep 2003 09:04:51 -0400 Received: from localhost (localhost [127.0.0.1]) by main.shu-bg.net (8.9.3/8.9.3) with ESMTP id QAA13155 for >ccl.net>; Wed, 3 Sep 2003 16:33:43 +0300 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0011_01C37234.5FFBA8E0" Date: Wed, 3 Sep 2003 15:59:35 +0300 From: "albena" >shu-bg.net> Message-ID: <001401c3721b$3ce91ea0$19800a0a<>shubg.net> MIME-Version: 1.0 Received: from oh408 (oh-408.shu-bg.net [10.10.128.25]) by main.shu-bg.net (AvMailGate-2.0.0.5) id 12995-4BC34DBF; Wed, 03 Sep 2003 16:33:33 +0300 Subject: CCL:to the GAMESS users To: >ccl.net> X-AntiVirus: OK! AntiVir MailGate Version 2.0.0.5 at main has not found any known virus in this email. X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 X-MSMail-Priority: Normal X-Priority: 3 This is a multi-part message in MIME format. ------=_NextPart_000_0011_01C37234.5FFBA8E0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: quoted-printable Dear CCLers, When I do HESSIAN job on already optimized geometry I need at least 6 = days in order to finish calculations. Unfortunately, it is quite rare to = have this time (because of many reasons) so my calculations are often = interrupted. Is there any possibility to accelerate calculations = (without changing hardware resources), to punch any information within = the working (interrupted!) files at the next job or to calculate on some = shared server?=20 There is an input groups as an example (just in case): $CONTRL SCFTYP=3DRHF MPLEVL=3D2 RUNTYP=3DHESSIAN COORD=3DZMT NZVAR=3D60 = $END $SYSTEM TIMLIM=3D10000 MEMORY=3D9000000 $END $BASIS GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 $END $GUESS GUESS=3DHUCKEL $END $FORCE METHOD=3DNUMERIC NVIB=3D1 DECOMP=3D.TRUE. PURIFY=3D.TRUE. TEMP(1)=3D363,373,383,393,403,413,423,433,443,453 $END $STATPT NSTEP=3D50 $END $DATA................ $END $ZMAT IZMAT(1)=3D...................... $END Thank you in advance. Best wishes, Albena Patleeva University of Shumen Shumen, Bulgaria, Universitetska 115 Email: a.patleeva<>shu-bg.net ------=_NextPart_000_0011_01C37234.5FFBA8E0 Content-Type: text/html; charset="koi8-r" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
 
When I do HESSIAN job on already = optimized=20 geometry I need at least 6 days in order to finish calculations.=20 Unfortunately, it is quite rare to have this time (because of many = reasons)=20 so my calculations are often interrupted. Is there any possibility to = accelerate=20 calculations (without changing hardware resources), to punch any = information=20 within the working (interrupted!) files at the next job or to = calculate=20 on some shared server?
 
There is an input groups as an example = (just in=20 case):
 
 $CONTRL SCFTYP=3DRHF MPLEVL=3D2 = RUNTYP=3DHESSIAN=20 COORD=3DZMT NZVAR=3D60 $END
 $SYSTEM TIMLIM=3D10000 = MEMORY=3D9000000=20 $END
 $BASIS  GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 = $END
 $GUESS=20 GUESS=3DHUCKEL $END
 $FORCE METHOD=3DNUMERIC NVIB=3D1 = DECOMP=3D.TRUE.=20 PURIFY=3D.TRUE.
TEMP(1)=3D363,373,383,393,403,413,423,433,443,453=20 $END
 $STATPT NSTEP=3D50=20 $END
 $DATA................
 $END
 $ZMAT &nb= sp;=20 IZMAT(1)=3D......................
 $END
Thank you in advance.

Best=20 wishes,

Albena Patleeva
University of Shumen
Shumen, = Bulgaria,=20 Universitetska 115
Email: >shu-bg.net">a.patleeva<>shu-bg.net
------=_NextPart_000_0011_01C37234.5FFBA8E0-- From chemistry-request@ccl.net Wed Sep 3 11:13:01 2003 Received: from thn.htu.se (adm.htu.se [193.10.192.40]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h83FD1qG006056 for ; Wed, 3 Sep 2003 11:13:01 -0400 Received: from webaccess.gw.htu.se ([193.10.198.231]) by thn.htu.se with esmtp (Exim 4.10) id 19uZJc-0006if-00 for chemistry-.at.-ccl.net; Wed, 03 Sep 2003 17:13:00 +0200 Received: from ROUTE-MTA by webaccess.gw.htu.se with Novell_GroupWise; Wed, 03 Sep 2003 17:12:59 +0200 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Wed, 03 Sep 2003 17:12:44 +0200 From: "Steven Kirk" To: Subject: Basis sets needed - 1,4-Benzenedithiol and (2-) ion Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline X-Scanner: exiscan for exim4 (http://duncanthrax.net/exiscan/) *19uZJc-0006if-00*fqNxmW1Oitw* Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h83FD1qG006057 Hello, I would be grateful if anyone who has good all-electron basis sets for the following molecule and its (2-) ion: Registry Number: 29878-58-8 CA Index Name: 1,4-Benzenedithiol could send them to me, or indicate an alternative location where I can find them. Many thanks in advance, Steve Kirk From chemistry-request@ccl.net Wed Sep 3 12:01:09 2003 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h83G18qG007578 for ; Wed, 3 Sep 2003 12:01:09 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Wed, 3 Sep 2003 13:03:49 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56BB8-.at.-correio.cetem.gov.br> From: Ian Hovell To: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= Subject: CCL: Optimising propylbenzene Date: Wed, 3 Sep 2003 13:03:48 -0300 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 h83G19qG007579 Dear CCLers, I have recently been trying to optimise propylbenzene at the B3LYP DFT level using a 6-31+g(d) basis set. I am using the tight options and an ultrafine grid in the G98w job route. This works great. But when I include the keyword option Freq=hindered the job fails claiming a problem in the number of degrees of freedom (DOF). On inspection on the coordinates of the benzene ring it can been seen that the C where the propyl group is attached is out of plane. And thus causing the problem I have with the DOF. I have tried manually correcting the coordinates and repeating the job but it reverts to the failing state. Can anyone shed some light on this problem? What do I need to do to to overcome this problem. I could simply remove the keyword option "hindered" but this would affect the absolute entropy value which I am looking for. TIA Ian Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cijncia e da Tecnologia- MCT Avenida Ipj, No 900 - Cidade Universitaria Ilha do Fundco Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell-.at.-cetem.gov.br From chemistry-request@ccl.net Wed Sep 3 12:48:33 2003 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h83GmWqG009041 for ; Wed, 3 Sep 2003 12:48:33 -0400 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Wed, 3 Sep 2003 17:48:29 +0100 Date: Wed, 3 Sep 2003 17:48:29 +0100 Message-ID: <3F335BC000012978^at^hawk.dcu.ie> From: "Noel O'Boyle" Subject: SCF convergence criteria To: chemistry^at^ccl.net 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 h83GmXqG009042 Hello all, This is a Gaussian 03 question. Does anybody know or understand why the default SCF convergence criteria for single point calculations is looser than the default for geometry optimisations? I would have expected them either to be the same for both (for consistency) or the opposite way around (since you can afford to spend more time on a single point convergence). In short, if you geometry optimise a structure, surely you should use SCF=Tight if you do a subsequent single point energy calculation. (Of course, you can avoid this question if you use Guess=Read.) Thanks, Noel O'Boyle From chemistry-request@ccl.net Wed Sep 3 15:49:21 2003 Received: from maties3.sun.ac.za (maties3.sun.ac.za [146.232.128.43]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h83JnKqG016052 for ; Wed, 3 Sep 2003 15:49:20 -0400 Received: from stbex01.stb.sun.ac.za ([146.232.20.16] helo=STBEVS01.stb.sun.ac.za) by maties3.sun.ac.za with esmtp (Exim 4.10) id 19udcs-0008BJ-00; Wed, 03 Sep 2003 21:49:10 +0200 X-MimeOLE: Produced By Microsoft Exchange V6.0.6375.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: CCl: RE: SCF convergence criteria Date: Wed, 3 Sep 2003 21:49:09 +0200 Message-ID: <972FCD6ABDC910478B716E1E29BA847313D4F9*at*STBEVS01.stb.sun.ac.za> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: SCF convergence criteria Thread-Index: AcNyT5QgxlFI44JjSWSGi/6CN6nQ4gAAy+ZQ From: "Dillen Jan " To: "Noel O'Boyle" Cc: X-Scanner: exiscan for exim4 (http://duncanthrax.net/exiscan/) *19udcs-0008BJ-00*8vWoJqWvCE6* Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h83JnLqG016053 Noel, If you are interested in the energy, your just want 1 number with reasonable accuracy. If your want to optimise the geometry, you need 1st derivatives of the energy w.r.t. the coordinates, in other words the change of the energy relative to a (very) small change in those coordinates. Hence you need that energy to be calculated more accurately because otherwise that relative change may be lost "in the noise". Although this explanation implicitly refers to numerical derivatives, the same argument holds for analytical ones. Groeten Jan > -----Original Message----- > From: Noel O'Boyle [mailto:noel.oboyle2*at*mail.dcu.ie] > Sent: 03 September 2003 18:48 > To: chemistry*at*ccl.net > Subject: CCL:SCF convergence criteria > > > Hello all, > This is a Gaussian 03 question. > > Does anybody know or understand why the default SCF > convergence criteria > for single point calculations is looser than the default for > geometry optimisations? > > I would have expected them either to be the same for both > (for consistency) > or the opposite way around (since you can afford to spend > more time on a > single point convergence). > > In short, if you geometry optimise a structure, surely you > should use SCF=Tight > if you do a subsequent single point energy calculation. (Of > course, you > can avoid this question if you use Guess=Read.) > > Thanks, > Noel O'Boyle > > > > > -= This is automatically added to each message by the mailing > script =- > To send e-mail to subscribers of CCL put the string CCL: on > your Subject: line > and send your message to: CHEMISTRY*at*ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST*at*ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the > maintainer: > Jan Labanowski, jkl*at*ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > >