From yubofan@guomai.sh.cn Mon Jun 16 08:49:17 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id IAA09157; Mon, 16 Jun 1997 08:33:30 -0400 (EDT) Received: from ------ ([210.0.0.14]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id UAA05547 for ; Mon, 16 Jun 1997 20:28:06 +0900 Message-Id: <199706161128.UAA05547@gm-email.guomai.sh.cn> From: "=?CN-GB?B?t7bT/bKo?=" To: Subject: Which Method is better for a rather big molecule? Date: Mon, 16 Jun 1997 00:28:43 +0800 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=CN-GB Content-Transfer-Encoding: 7bit Hi, All, I want to optimize the conformations of some big molecules, for example, N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable for this kind big system. Also, some semi-empirical methods are not accurate enough for such calculations. Which method can do this kind work? Thank you very much! Y. FAN From s.hogg@ic.ac.uk Mon Jun 16 09:49:18 1997 Received: from romeo.ic.ac.uk for s.hogg@ic.ac.uk by www.ccl.net (8.8.3/950822.1) id IAA09123; Mon, 16 Jun 1997 08:27:38 -0400 (EDT) Received: from judy.ic.ac.uk [155.198.5.5] by romeo.ic.ac.uk with esmtp (Exim 1.62 #1) id 0wdasc-00055B-02; Mon, 16 Jun 1997 13:27:30 +0100 Received: from mtcmsa.mt.ic.ac.uk (root@mtcmsag1.mt.ic.ac.uk [155.198.96.22]) by judy.ic.ac.uk (8.7.5/8.7.5) with SMTP id NAA14439 for ; Mon, 16 Jun 1997 13:27:26 +0100 (BST) Received: from mtcsh.mt.ic.ac.uk by mtcmsa.mt.ic.ac.uk (5.x/4.1) id AA19101; Mon, 16 Jun 1997 13:27:24 +0100 X-Received: from helen.mt.ic.ac.uk (dialup-1-1.net.ic.ac.uk) by mtcsh.mt.ic.ac.uk; Mon, 16 Jun 1997 13:27:22 +0100 Message-Id: <3.0.1.32.19970616132559.006e846c@155.198.100.1> X-Sender: seth@155.198.100.1 X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Mon, 16 Jun 1997 13:25:59 +0100 To: chemistry@www.ccl.net From: Simon Hogg Subject: TINKER mailing list / information ?? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Is there such a thing as a TINKER mailing list? Or to put it another way, how many people are using the TINKER package (by Stephen Jay Ponder, http://dasher.ustl.edu/tinker ). Is anyone able to offer advice / help for this very useful program? -- Simon Hogg, Imperial College, London, UK Tel. +44 171 589 5111 ext. 56721 Fax. +44 171 584 3194 Email: s.hogg@ic.ac.uk Glass-List: glass-list@ic.ac.uk From joubert@ext.jussieu.fr Mon Jun 16 10:49:17 1997 Received: from shiva.jussieu.fr for joubert@ext.jussieu.fr by www.ccl.net (8.8.3/950822.1) id JAA09719; Mon, 16 Jun 1997 09:58:18 -0400 (EDT) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.8.5/jtpda-5.2) with ESMTP id PAA26657 for ; Mon, 16 Jun 1997 15:57:46 +0200 (METDST) Received: from [134.157.11.17] by idf.ext.jussieu.fr (8.8.5/jtpda-4.0) with SMTP; Mon, 16 Jun 1997 15:57:38 +0200 (METDST) X-Sender: joubert@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 16 Jun 1997 16:00:37 +0200 To: chemistry@www.ccl.net From: joubert@ext.jussieu.fr (Laurent Joubert) Subject: Compiling G94 on a SGI O2 workstation Dear Netters, I'm actually trying to compile Gaussian94 on a O2 workstation. I know that the O2 cannot execute 64 bits executable files (-64 option). Therefore, I modified the sgi.make file in order to compile the program with the -n32 option. The compilation was successful. However, an error occurs when I try to run a job : bogus memory allocation error. What can I do ? Thanks in advance for your help. Laurent Joubert ******************************************************** * Laurent JOUBERT (PhD student) * * * * Ecole Nationale Superieure de Chimie de Paris * * Laboratoire d'Electrochimie et de Chimie Analytique * * 11, rue Pierre et Marie Curie * * 75231 PARIS CEDEX 05- FRANCE * * * * Tel : (33) 01-44-27-66-94 * * Fax : (33) 01-44-27-67-50 * * * * E-Mail : joubert@ext.jussieu.fr * * http://www.enscp.jussieu.fr * ******************************************************** From i1s@email.psu.edu Mon Jun 16 11:49:20 1997 Received: from f01n05.cac.psu.edu for i1s@email.psu.edu by www.ccl.net (8.8.3/950822.1) id LAA10450; Mon, 16 Jun 1997 11:35:23 -0400 (EDT) Received: from [146.186.73.41] (I1S.OZ.PSU.EDU [146.186.73.41]) by f01n05.cac.psu.edu (8.7.6/8.6.12) with SMTP id LAA21370 for ; Mon, 16 Jun 1997 11:35:22 -0400 Message-Id: <199706161535.LAA21370@f01n05.cac.psu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 16 Jun 1997 12:27:56 -0400 To: chemistry@www.ccl.net From: i1s@psu.edu (Inge Schuster) Subject: MacNMR Hi! Where can I obtain the program, MacNMR, which converts FID's to NMR spectra and allows their subsequent manipulation? inge schuster I1S@psu.edu From buyong@ibmnla.chem.uga.edu Mon Jun 16 12:49:20 1997 Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id MAA10930; Mon, 16 Jun 1997 12:25:55 -0400 (EDT) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id MAA20004; Mon, 16 Jun 1997 12:25:56 -0400 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA17862; Mon, 16 Jun 1997 12:25:38 -0400 Date: Mon, 16 Jun 1997 12:25:33 -0400 (EDT) To: =?CN-GB?B?t7bT/bKo?= Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Which Method is better for a rather big molecule? In-Reply-To: <199706161128.UAA05547@gm-email.guomai.sh.cn> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE =09You may use RHF with small basis sets. However, it still depends how many memory your computer has. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D On Mon, 16 Jun 1997, [CN-GB] =B7=B6=D3=FD=B2=A8 wrote: > Hi, All, >=20 > I want to optimize the conformations of some big molecules, for example, > N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable > for this kind big system. Also, some semi-empirical methods are not=20 > accurate enough for such calculations. >=20 > Which method can do this kind work? >=20 >=20 > Thank you very much! >=20 > Y. FAN >=20 > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: yubofan@guomai.sh.cn > -- Original Sender From: Address: yubofan@guomai.sh.cn > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordin= ator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net= 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html=20 >=20 >=20 From genghis@darkwing.uoregon.edu Mon Jun 16 17:49:30 1997 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.3/950822.1) id RAA13961; Mon, 16 Jun 1997 17:14:15 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.5/8.8.5) with SMTP id OAA15493 for ; Mon, 16 Jun 1997 14:13:54 -0700 (PDT) Date: Mon, 16 Jun 1997 14:13:46 -0700 (PDT) From: Dale Andrew Braden To: cclpost Subject: Summary: wfn stability Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, I recently posted a question about RHF wavefunction instability. Most of the responses addressed the problem of spin contamination rather than wavefunction stability, but these two are interrelated anyhow. Useful references for these two topics are given at the end of this post. I thank all of those who responded! Some of the respondents felt that this "problem" was not terribly serious, because much more sophisticated ab initio methods are available now that are not as fraught with problems as HF. I am inclined to agree with this now. Consider benzene. I optimized the geometry at the RHF/6-31+G* level, and found that the final wfn had a RHF-->UHF instability. I then reoptimized the wfn at the UHF level, and found that the energy decreased, and spin contamination was introduced, as expected. The problem with the spin contamination, from an experimentalist's point of view, is that this UHF description of benzene indicates that, for example, it would give an ESR signal, because the spin density around the nuclei is no longer zero. This is an unrealistic description of benzene. People have tried to salvage the situation by projecting out the contaminating states of higher multiplicity, but the resulting wfn is no longer optimized with respect to the original parameters. I suppose the best one can do if HF theory must be used is to stick with the RHF wfn and simply say that it has an instability. The point I wanted to make is that, although the use of RHF/UHF/ROHF/PUHF techniques is perhaps decreasing, the use of Moller-Plesset perturbation methods is, I think, still very common. Since MPx perturbations are carried out on HF wavefunctions, the MPx results are also affected by stability/contamination problems. I think this is more serious, especially if RHF-->UHF instabilities are as common as Chambaud et al. (ref. below) indicate. One last point, which was made by one of the respondents. Typically, the hamiltonian (or Fock operator) includes no energy terms that depend upon electron spin (like a spin-orbit operator). This means that spin energetics are not included in the "optimized" wfn, which is determined when the total energy stops changing in the SCF calculation. Thus spin energetics do not play a role in determining the final spin distribution in the molecule. (Spin-orbit coupling is assumed to be small for many molecules, but it can be large for organometallics.) From this point of view, spin "contamination" is not only arbitrarily defined, but quite meaningless. For wfn stability, see the following references (and references therein!): Chambaud, Levy, and Millie; Theor. Chim. Acta 48 (1978) 103. Schlegel and McDouall in Computational Advances in Organic Chemistry; Ogretir and Csizmadia, eds. Kluwer 1991. Ma, Wong, Paddon-Row, and Li; Chem. Phys. Lett. 213 (1993) 189. For spin contamination: Nandi, Kar, and Sannigrahi; Theochem 362 (1996) 69. (And refs. therein!). Cheers to all, Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From ahocquet@tamarugo.cec.uchile.cl Mon Jun 16 18:49:22 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id RAA14108; Mon, 16 Jun 1997 17:51:14 -0400 (EDT) Received: from 146.83.5.131 ([146.83.10.67]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA08009; Mon, 16 Jun 1997 17:52:40 +0400 Date: Mon, 16 Jun 1997 17:52:40 +0400 Message-Id: <9706162152.AA08009@tamarugo.cec.uchile.cl> X-Sender: ahocquet@tamarugo.cec.uchile.cl X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Alexandre Hocquet Subject: semantics : molecular modelling Dear CCLers, While Boyd and Lipkowitz once intended to review definitions of "computational chemistry" (Reviews in Computational Chemistry, Vol 1, page vii), the words "molecular modelling" still appear confusing to me : While it seems logical to think that "molecular modelling" is that part of "computational chemistry" that describes behaviour of molecules by the formalism of some theoretical model, there seems to exist in the community a much more restrictive use of "molecular modelling". This second definition could be "Use of any non quantum mechanics model to describe the behaviour of molecules". If one looks at the scope of the Journal of Molecular Modeling, no semi empirical, ab initio, dft methods are quoted, while the general guidelines state that "The Journal of Molecular Modeling will cover all aspects of computational chemistry". Another example, the ICCCRE XII congress divides the scientific program in different topics. Amongst them : - Semi empirical and Ab initio quantum chemistry, dft methods - Molecular Modeling, QSAR Any hints on a proper definition ? Any historical reason for different uses of "molecular modelling" ? And, above all, one or two l ? Facultad de Ciencias Fisicas Universidad de Chile Blanco Encalada, 2008 Santiago Centro CHILE fono : 56 2 678 45 19 fax : 56 2 696 73 59