From chemistry-request@server.ccl.net Wed Nov 28 06:59:00 2001 Received: from nori.rl.ac.uk ([130.246.135.154]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fASBwxB08325 for ; Wed, 28 Nov 2001 06:59:00 -0500 Received: from kohn.nd.rl.ac.uk.nd.rl.ac.uk ([130.246.48.218]) by nori.rl.ac.uk (8.11.1/8.11.1) with ESMTP id fASBwrR32148 for ; Wed, 28 Nov 2001 11:58:53 GMT MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <15364.53498.709743.826422@kohn.nd.rl.ac.uk> Date: Wed, 28 Nov 2001 11:56:42 +0000 To: chemistry@ccl.net Subject: CHARMM and other parameters on WWW? X-Mailer: VM 6.97-rfhacked under 21.4 (patch 4) "Artificial Intelligence" XEmacs Lucid From: "Keith Refson" Does anyone know of any online availability of the forcefield parameters for CHARMM and/or other forcefields suitable for small organic molecules. (I probably just need C, H, S, N, O). Keith Refson -- Dr Keith Refson, Building R3 Rutherford Appleton Laboratory Chilton Didcot Oxfordshire OX11 0QX T: 01235 446652 K.Refson@ F: 01235 445720 @rl.ac.uk From chemistry-request@server.ccl.net Wed Nov 28 01:23:32 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAS6NWB01851 for ; Wed, 28 Nov 2001 01:23:32 -0500 Received: from [128.97.147.217] (ch-17.psnet.ucla.edu [128.97.147.217]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id fAS6NPC13982 for ; Tue, 27 Nov 2001 22:23:25 -0800 (PST) Mime-Version: 1.0 Message-Id: Date: Tue, 27 Nov 2001 22:23:08 -0800 To: ccl From: Eric Scerri Subject: collation of responses on ab initio/first principles Content-Type: text/plain; charset="us-ascii" ; format="flowed" Here as promised are responses to my question (see end of this posting) about the terms 'ab initio' and 'first principles'. Thanks to respondents. I was not so much interested in the origin of the term ab initio but of course the answers are interesting. My real aim was to discover whether there is an intended subtle shift in meaning in using "first principles" rather than ab initio. None of the responses indicate that this might be so. This idea arose from a recent conversation I had with Roald Hoffman who implied that this is the case. Also, I was particularly interested in the posting from Per Ola Norrby who discusses how basis sets are constructed in a semi-empirical manner especially regarding expansion coefficients and contraction. I would be interested in learning more about this aspect and/or references to where it is discussed in the literature. Further comments to me on any of these issues are welcome. eric scerri ------------------------------------------- ------------------------------------------------------------ Date: Mon, 26 Nov 2001 15:25:41 +0000 (GMT) From: Stuart Purdie X-Sender: sdjp@st-and.ac.uk To: Eric Scerri Subject: Re: CCL:usage of terms "ab initio" and "first principles" Status: RO As I use the terms, they are interchangeable, meaning that the calculations are performed without recourse to any experimental measurent. This would include Hartree-Fock, and many of the DFT functionals, along with quantum monte carlo and CI methods. In actuallity, I belive they are taken to include all DFT, rather than spliting that particular hair. First principle seems to be used because the latin in ab initio can been seen as unnessecerily elitist. Stuart Purdie School of Chemistry University of St Andrews -------------------------------------- Date: Sat, 24 Nov 2001 12:39:04 -0500 From: elewars Subject: CCL:usage of terms "ab initio" and "first principles" To: chemistry@ccl.net X-Accept-Language: en Sender: "Computational Chemistry List" Status: RO 2001 nov 24 Hello, Re the term _ab initio_", Dewar said: ""The term ab initio was originally applied to the Roothaan=Hall (RH) approach through an amusing accident. Parr was collaborating in some work of this kind with a group in England. In reporting one of his calculations, he described it as "ab initio", implying that the whole of that particular project had been carried out from the beginning in his laboratory. The term, unfortunately, became ..." See M. J. S. Dewar, "A Semiempirical Life", ACS, Washington, DC, 1992; p. 129 (series Profiles, Pathways and Dreams, autobiographies of eminent chemists). Dewar was the leading champion of semiempirical methods over ab initio ones, and I do not know if Robert Parr ever commented on the above account. I don't know if "first principles" was introduced to play down the claim that ab initio is purely theoretical; certainly high-accuracy methods like G2 and G3 are calibrated with experimental data, something which would have amused Dewar. E. Lewars ====== ---------------------------------------- Hi Eric, This is not what you asked for, but I want to throw in a quick thought about those "empirical" parameters in DFT. It's not always realised that what is called "ab initio" incorporates many empirical parameters. For example, a standard HF/6-31G* calculation would be called "ab initio", but all the exponents and contraction coefficients in the basis set were selected by fitting to experimental data! That's one of the main reasons for the success of the Pople basis sets, they have been fit to real data, thus they are good at reproducing real data. The effect, of course, is that the basis set incorporates systematical errors that to a large extent cancels the systematical errors in HF ... Thus, if you do a HF/6-31G* calculation on a standard organic molecule, you implicitly use 20-30 parameters that have been fit to experiment. If you instead use B3LYP, you add three more parameters. I don't think the difference between, for example, 30 and 33 parameters is sufficient to introduce a distinction in the degree of "empiricalness" of the methods. Naturally, the above is not limited to the Pople sets. Any basis set with fixed exponent and/or contraction coefficients have at some point been adjusted to fit some data. I'm not completely sure, but I think that the main difference is that the Pople parameterization of basis sets used molecular data, whereas most others use atomic data. Thus, the Pople sets are good for molecules, whereas others of the same size are better for atoms. I have yet not seen a true "ab initio" calculation for a molecule of a size that interests me... Best, Per-Ola -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/ Technical University of Denmark, Dept. of Chem., Org. Chem. Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon@kemi.dtu.dk tel +45-45252123, fax +45-45933968 ----------------- Date: Sat, 24 Nov 2001 11:17:59 +0100 From: Thomas.Heine@chiphy.unige.ch Subject: Re: CCL:usage of terms "ab initio" and "first principles" To: Eric Scerri X-Comment: This message was scanned against viruses by lima.unige.ch. Status: RO Dear Eric, in my experience first principles was mainly used by physicists, already in times DFT was not in fashion in chemistry. Chemists used ab initio these days for everything HF-like and beyond. When chemists discovered DFT some of them started to use first principles to characterise their DFT calculations, especially those using CPMD. Perhaps to avoid confusion? I think it's similar for the use of SCF, which means in chemistry HF, and in physics simply the technique of solving the KS (or, if you want HF) equations. Have a nice weekend Thomas ------------------------------------------------- X-Sender: sabrash@facstaff.richmond.edu Date: Sat, 24 Nov 2001 01:54:54 -0500 To: Eric Scerri From: "Samuel A. Abrash" Subject: Re: CCL:usage of terms "ab initio" and "first principles" Status: RO Eric, First principles has been used for a long time, as a vernacular alternative to ab initio. The distinction you're talking about may be recent. Freed, though, would say that DFT is semiempirical. Best, Sam Abrash At 10:17 PM 11/23/01 -0800, you wrote: > >I am interested in discovering the origins and current usage of the terms >"ab initio" and "first principles" in computational work. > >Am I correct in thinking that the latter was introduced relatively >recently, because one can no longer claim that practically >implemented DFT methods are truly ab initio given the 'fixing' of >density gradients by reference to experimental data. > >So although in terms of translation the two terms are virtually >synonymous the usage implies that "first principles" is not quite so >"ab initio"? > >I would appreciate comments and/or references to articles which may >have discussed this question or first suggested such terminology >regarding "first principles" as an alternative. I will post >responses. > > Eric Scerri , -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri@chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.wkap.nl/prod/j/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@server.ccl.net Wed Nov 28 10:45:22 2001 Received: from ck-sg.p.lodz.pl ([212.51.207.68]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fASFjLB12221 for ; Wed, 28 Nov 2001 10:45:21 -0500 Received: from wiedzmin (pc-212-51-214-182.p.lodz.pl [212.51.214.182]) by ck-sg.p.lodz.pl (SGI-8.9.3/8.9.3) with SMTP id QAA65427 for ; Wed, 28 Nov 2001 16:50:11 +0100 (MET) Message-ID: <009a01c17823$b8a082c0$b6d633d4@p.lodz.pl> From: "Piotr Paneth" To: Subject: cobalt Date: Wed, 28 Nov 2001 16:45:35 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Since we're on MM parameters: we're looking for a good parametrization of Co in B12 or similar compounds for OPLS(-AA), CHARMM, or Amber (in this order of preference). Any pointers appreciated. Cheers, Piotr **************************** Prof. Piotr Paneth Institute of Applied Radiation Chemistry Technical University of Lodz Zeromskiego 116, 90-924 Lodz, Poland phone: (+48 42) 631-3199 fax: (+48 42) 636-5008 From chemistry-request@server.ccl.net Wed Nov 28 12:59:38 2001 Received: from mail.rpi.edu (root@[128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fASHxcB14255 for ; Wed, 28 Nov 2001 12:59:38 -0500 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by mail.rpi.edu (8.11.3/8.11.3) with ESMTP id fASHxWV69116; Wed, 28 Nov 2001 12:59:32 -0500 Message-Id: <200111281759.fASHxWV69116@mail.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: scerri@chem.ucla.edu From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute Cc: chemistry@ccl.net X-Originating-Ip: 128.113.21.67 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Wed, 28 Nov 2001 12:59:31 EST X-Mailer: EMUmail 4.00 Subject: Re: CCL:collation of responses on ab initio/first principles On Tue, 27 Nov 2001 22:23:08 -0800 Eric Scerri wrote: > > Also, I was particularly interested in the posting from Per Ola > Norrby who discusses how basis sets are constructed in a > semi-empirical manner especially regarding expansion coefficients and > contraction. I would be interested in learning more about this > aspect and/or references to where it is discussed in the literature. > > Further comments to me on any of these issues are welcome. > It is my underdstanding that the term "ab initio" simply means that all atomic/molecular INTEGRALS are computed analytically, without recourse to empirical parametrization. It DOES NOT imply that the method is exact nor that the basis set contraction coefficients were obtained without recourse to parametrization. See, e.g. Frank L. Pilar, "Elementary Quantum Chemistry" (McGraw Hill, NY, 1968) Chapter 16, page 453. Even the integrals need NOT be evaluated EXACTLY for a method to be called ab initio. For instance, Gaussian employs several asymptotic and other cutoffs to approximate integral evaluation. The application of the terminology to DFT is justified on the grounds that while the FUNCTIONALS may be obtained with recourse to parametrization, the INTEGRALS are evaluated analytically. Dr. N. Sukumar Rensselaer Department of Chemistry From chemistry-request@server.ccl.net Wed Nov 28 12:23:27 2001 Received: from uscmail.usc.es ([193.144.75.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fASHNLB13702 for ; Wed, 28 Nov 2001 12:23:21 -0500 Received: from qfcronos (qfcronos.usc.es [193.144.74.154]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id SAA20591 for ; Wed, 28 Nov 2001 18:23:15 +0100 (MET) Message-ID: <000c01c17831$fe4d6460$9a4a90c1@usc.es> From: =?iso-8859-1?Q?Jes=FAs_Rodr=EDguez_Otero?= To: Subject: CADPAC for Linux Date: Wed, 28 Nov 2001 18:27:44 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C1783A.5F69F3A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C1783A.5F69F3A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters, Does somebody knows if it is possible to run CADPAC under Linux, with = g77 or any other compiler? I was trying to do so in a PIII PC, but I have a lot of problems. Also, I compiled CADPAC with compaq fortran for alpha under Linux, but = when I try to calculate polarisabilituies, the program crashes, with the = following message: Dipole Moment in atomic units x y z Electronic 0.00000000 0.00000000 4.23615019 Nuclear 0.00000000 0.00000000 -4.58139913 Total 0.00000000 0.00000000 -0.34524894 Dipole Moment 0.34524894 In Debyes x y z Electronic 0.00000000 0.00000000 10.76722526 Nuclear 0.00000000 0.00000000 -11.64476098 Total 0.00000000 0.00000000 -0.87753572 Dipole Moment 0.87753572 Construction of right-hand-side of equations completed In-core CHF forrtl: error (65): floating invalid thanks in advance ------=_NextPart_000_0009_01C1783A.5F69F3A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear netters,
 
Does somebody knows if it is possible = to run CADPAC=20 under Linux, with g77 or any other compiler?
I was trying to do so in a PIII PC, but = I have a=20 lot of problems.
 
Also, I compiled CADPAC with compaq = fortran for=20 alpha under Linux, but when I try to calculate polarisabilituies, the = program=20 crashes, with the following message:
          &nbs= p;         =20 Dipole Moment in atomic units
 
 
          &nbs= p;         =20 x            =   =20 y            =   =20 z
 Electronic     =20 0.00000000     =20 0.00000000     =20 4.23615019
 Nuclear       &nbs= p;=20 0.00000000      = 0.00000000    =20 -4.58139913
 Total        = ;  =20 0.00000000      = 0.00000000    =20 -0.34524894
 Dipole Moment    =20 0.34524894
 
          &nbs= p;         =20 In Debyes
 
          &nbs= p;         =20 x            =   =20 y            =   =20 z
 Electronic     =20 0.00000000      = 0.00000000    =20 10.76722526
 Nuclear       &nb= sp;=20 0.00000000      0.00000000   =20 -11.64476098
 Total       &nbs= p;  =20 0.00000000      = 0.00000000    =20 -0.87753572
 Dipole Moment    =20 0.87753572
 Construction of right-hand-side of equations=20 completed
 In-core CHF
forrtl: error (65): floating=20 invalid
 
 
thanks in = advance
------=_NextPart_000_0009_01C1783A.5F69F3A0-- From chemistry-request@server.ccl.net Wed Nov 28 12:53:40 2001 Received: from rbadb2.rbacpxclu.bas.roche.com ([196.3.50.241]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fASHreB14167 for ; Wed, 28 Nov 2001 12:53:40 -0500 Received: from CONVERSION-DAEMON.Roche.COM by Roche.COM (PMDF V6.0-025 #47170) id <01KB8XIT0KU897F640@Roche.COM> for chemistry@ccl.net; Wed, 28 Nov 2001 18:51:41 +0100 Received: from rbamsemcn1.bas.roche.com (rbamsemcn1.bas.roche.com [145.245.211.139]) by Roche.COM (PMDF V6.0-025 #47170) with ESMTP id <01KB8XIS48BY9AW27L@Roche.COM> for chemistry@ccl.net; Wed, 28 Nov 2001 18:51:36 +0100 Received: by rbamsemcn1.bas.roche.com with Internet Mail Service (5.5.2653.19) id ; Wed, 28 Nov 2001 18:52:10 +0100 Content-return: allowed Date: Wed, 28 Nov 2001 18:52:03 +0100 From: "Borosy, Andras {Basi~Basel}" Subject: Spartan vs Gaussian To: "'chemistry@ccl.net'" Message-id: <5FBD82D1CB46D511AAEA0002A55C6F5202AAA968@rbamsem3.bas.roche.com> 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 fASHreB14168 Deat Colleague, Spartan has been dedicated for computational medicinal and organic chemsitry. It is cheaper then Gaussian, but much more userfriend and has a decent graphics. If you need model d and f field compounds and/or you have more money, buy Gaussian! If you have much more money, buy Jaguar! Best wishes, András Borosy Basilea Pharmaceutica Ltd POB 3255, 65/316B 4002 Basel tel: +41-61-6885469 fax: +41-61-6882139 www.basileapharma.com