From luca@lcfs.chim.unifi.it Mon Jan 27 03:19:23 1997 Received: from cesit1.unifi.it for luca@lcfs.chim.unifi.it by www.ccl.net (8.8.3/950822.1) id CAA05340; Mon, 27 Jan 1997 02:33:59 -0500 (EST) Received: from 193.52.207.118 (193.52.207.118) by CESIT1.UNIFI.IT (PMDF V5.0-4 #3688) id <01IEP9AOOCCG000VXS@CESIT1.UNIFI.IT> for chemistry@www.ccl.net; Mon, 27 Jan 1997 08:33:41 +0100 (MET) Date: Mon, 27 Jan 1997 08:38:14 +0100 From: "Dr. Luca Pedocchi" Subject: Re: CCL:MolDraw manual? X-Sender: "Dr. Luca Pedocchi" To: chemistry@www.ccl.net Reply-to: luca@lcfs.chim.unifi.it Message-id: <32EC5B66.1C7B@lcfs.chim.unifi.it> Organization: Dipartimento di Chimica - Firenze MIME-version: 1.0 X-Mailer: Mozilla 4.0b1 (Win95; I) Content-type: multipart/alternative; boundary="----------1E5753B366BA1" Content-transfer-encoding: 7BIT X-Priority: Normal References: ------------1E5753B366BA1 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Dear Irena, if you are speaking of MolDraw from University of Turin, there is a www page at http://www.ch.unito.it/ch/DipIFM/Software/MOLDRAW/moldraw.html Regards Luca -- Dr. Luca Pedocchi Laboratorio di Chimica Fisica delle Interfasi via Cavour, 82 - 50129 Firenze - ITALY http://lcfs.chim.unifi.it/solid/pedocchi e-mail luca@lcfs.chim.unifi.it phone +39-55-2757793 fax +39-55-219802 Non esistono uomini cattivi, se sono cucinati bene (Stefano Benni) ------------1E5753B366BA1 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii

Dear Irena, if you are speaking of MolDraw from University of Turin, there is a www page at http://www.ch.unito.it/ch/DipIFM/Software/MOLDRAW/moldraw.html

Regards

                        Luca
--

Dr. Luca Pedocchi
Laboratorio di Chimica Fisica delle Interfasi
via Cavour, 82 - 50129 Firenze - ITALY

http://lcfs.chim.unifi.it/solid/pedocchi
e-mail luca@lcfs.chim.unifi.it

phone +39-55-2757793
fax   +39-55-219802

Non esistono uomini cattivi, se sono cucinati bene
                                            (Stefano Benni)

------------1E5753B366BA1-- From lrbu00@xd88.kodak.com Mon Jan 27 09:19:10 1997 Received: from kodakr.kodak.com for lrbu00@xd88.kodak.com by www.ccl.net (8.8.3/950822.1) id JAA11999; Mon, 27 Jan 1997 09:15:49 -0500 (EST) From: Received: from euler.kodak.com by kodakr.kodak.com with SMTP id AA02520 (5.67b/IDA-1.5 for <@kodakr.kodak.com:chemistry@www.ccl.net>); Mon, 27 Jan 1997 09:14:28 -0500 Received: from xd88.kodak.com by euler.kodak.com via SMTP (940816.SGI.8.6.9/940406.SGI) id JAA23495; Mon, 27 Jan 1997 09:15:20 -0500 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA19585; Mon, 27 Jan 1997 09:15:20 -0500 Date: Mon, 27 Jan 1997 09:15:20 -0500 Message-Id: <9701270915.ZM12927@xd88.kodak.com> X-Mailer: Z-Mail (3.0.0 15dec93) To: chemistry@www.ccl.net Subject: Banal Fortran Question Cc: McKelvey@kodakr.kodak.com Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 CCLER's: I am trying to write a program to take external information and feed it into HYPERCHEM. One theing that the HYPERCHEM ".ext" file requires is that some input lines be terminated with a \ (backslash). The "obvious" way to to write a backslash in a format statement does not seem to work, i.e. ''\'' , does not work as the \ is interpreted by the compiler (both on rs6000 and sgi r8000) and gives an error. Any hints? Thanks! John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From dsmith@CTCnet.Net Mon Jan 27 09:25:55 1997 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id IAA11825; Mon, 27 Jan 1997 08:51:04 -0500 (EST) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id IAA25289; Mon, 27 Jan 1997 08:47:25 -0500 Date: Mon, 27 Jan 1997 08:47:25 -0500 Message-Id: <199701271347.IAA25289@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: basis set balance? In the spirit of Jan's recent request for more teaching, I wholeheartedly agree! So, I have a need to learn something, and perhaps replies can be sent directly to the list, not to me, so as to foster interactive conversation (not enough of that anymore, it seems, appears here). The question: Can people please explain the concept of having a balanced basis set and the dangers inherent in an unbalanced set? In particular, why can I not simply use a large basis, including extra split valance functions, polarization and diffuse functions, only on the atoms I need them on, and a smaller, more compact basis set on the "unimportant" atoms to my chemical question? This would certainly save time and resources during the calculation. Doug -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology. From Sylvie.Joanteguy@univ-pau.fr Mon Jan 27 10:19:10 1997 Received: from crisv2.univ-pau.fr for Sylvie.Joanteguy@univ-pau.fr by www.ccl.net (8.8.3/950822.1) id JAA12528; Mon, 27 Jan 1997 09:52:40 -0500 (EST) From: Received: from crisv3.univ-pau.fr by crisv2.univ-pau.fr; Mon, 27 Jan 1997 15:52:22 +0100 Received: by crisv3.univ-pau.fr; Mon, 27 Jan 1997 15:52:22 +0100 Date: Mon, 27 Jan 1997 15:52:22 +0100 Message-Id: <199701271452.PAA37020@crisv3.univ-pau.fr> To: chemistry@www.ccl.net Subject: DFT Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-MD5: P5slPfMXgLiqsKXNsnceBw== Hello everybody, My problem is the calculation of ionization potentials in DFT I don't understand two points: 1- Koopmans theorem in DFT and its application: why it doesnt work? 2- what represents rreally khon-sham orbitals-Are they any significations? (if not why ? ) many thanks Sylvie Joanteguy e-mail:joan@univ-pau.fr From hinsen@lmspc2.ibs.fr Mon Jan 27 11:19:11 1997 Received: from ibs.ibs.fr for hinsen@lmspc2.ibs.fr by www.ccl.net (8.8.3/950822.1) id KAA13072; Mon, 27 Jan 1997 10:53:23 -0500 (EST) Received: from lmspc2.ibs.fr (hinsen@lmspc2.ibs.fr [192.134.36.142]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id QAA07711; Mon, 27 Jan 1997 16:53:57 +0100 Received: (from hinsen@localhost) by lmspc2.ibs.fr (8.8.5/8.8.5) id QAA29583; Mon, 27 Jan 1997 16:51:08 +0100 Date: Mon, 27 Jan 1997 16:51:08 +0100 Message-Id: <199701271551.QAA29583@lmspc2.ibs.fr> From: Konrad Hinsen To: laaksone@csc.fi CC: berriz@chasma.harvard.edu, chemistry@www.ccl.net In-reply-to: (message from Leif Laaksonen on Sat, 25 Jan 1997 10:58:34 +0200 (EET)) Subject: Re: CCL:Quanta, Alphas & Xterms (Was: "Running Quanta remotely" & "Quanta on AlphaStation clones?") > software than for the hardware. In fact I see the reluctance, by the > software houses, to port applications to the DEC platform as the last > desperate attempt to only support Unix versions, because DEC is also > active in the Win NT field. You can support DEC's Unix without supporting DEC's Windows machines; they are completely unrelated. In fact, I see no reason to assume any malicious behaviour in only supporting selected machines. Each additional platform costs quite a bit of money in development and support, so there are good economic reasons for keeping the number of systems to a minimum. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From jdurant@mephisto.ca.sandia.gov Mon Jan 27 11:30:44 1997 Received: from mephisto.ca.sandia.gov for jdurant@mephisto.ca.sandia.gov by www.ccl.net (8.8.3/950822.1) id KAA13083; Mon, 27 Jan 1997 10:55:08 -0500 (EST) Received: by mephisto.ca.sandia.gov (950413.SGI.8.6.12/890607.SGI) (for chemistry@www.ccl.net) id PAA16623; Mon, 27 Jan 1997 15:54:20 GMT From: jdurant@mephisto.ca.sandia.gov (Joe Durant) Message-Id: <199701271554.PAA16623@mephisto.ca.sandia.gov> Subject: CCL:G:BhandhLYP To: chemistry@www.ccl.net Date: Mon, 27 Jan 1997 07:54:20 -0800 (PST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi John! You asked about the status of Becke's half and half functional, as implemented by Gaussian. I am mainly concerned with calculating transition states, and find that it is the only functional implemented by Gaussian that does not systematically underpredict barrier heights. You are correct in noting that Gaussian's implementation is not in keeping with Becke's; I would be interested in knowing how well Gaussian's implementation performs on the "G2 set" of molecules. (I would be grateful to anybody who forwards me a set of z-matrices for these molecules!). Gaussian eliminated the option in the first couple of releases of G94 (although you can still specify it explicitly); they recanted and have reinstated it in the more recent releases. In summary, BHandHLYP seems to have some advantages; while not perfect it is my first choice for calculating transition state properties. Joe -- #################################################################### # Joe Durant voice: (510) 294-3343 # # Mail Stop 9057 FAX: (510) 294-2276 # # Sandia National Laboratories jdurant@ca.sandia.gov # # Livermore, CA 94551 http://mephisto.ca.sandia.gov # #################################################################### From hinsen@lmspc2.ibs.fr Mon Jan 27 11:32:19 1997 Received: from ibs.ibs.fr for hinsen@lmspc2.ibs.fr by www.ccl.net (8.8.3/950822.1) id KAA13030; Mon, 27 Jan 1997 10:47:10 -0500 (EST) Received: from lmspc2.ibs.fr (hinsen@lmspc2.ibs.fr [192.134.36.142]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id QAA07668; Mon, 27 Jan 1997 16:48:13 +0100 Received: (from hinsen@localhost) by lmspc2.ibs.fr (8.8.5/8.8.5) id QAA29562; Mon, 27 Jan 1997 16:45:24 +0100 Date: Mon, 27 Jan 1997 16:45:24 +0100 Message-Id: <199701271545.QAA29562@lmspc2.ibs.fr> From: Konrad Hinsen To: D.van.der.Spoel@chem.rug.nl CC: chemistry@www.ccl.net In-reply-to: <199701252150.WAA11355@rugmd2> (D.van.der.Spoel@chem.rug.nl) Subject: Re: CCL:Quanta etc. > Although these packages may require some more work to get running, > but you can run the software on any machine you like. Some examples: > Visualisation: check out VMD (http://www.ks.uiuc.edu) Works only on SGIs and HPs, according to the Web page... In fact, of all free visualization programs I am aware of, only RasMol works on a large range of hardware without special tricks. And while RasMol works fine for what it was intended for, it lacks some features that would often be useful (such as animation). > Molecular Dynamics: check out GROMACS (http://rugmd0.chem.rug.nl/~gmx) > Ab Initio: check out GAMESS Unfortunately, most of these "academic" codes suffer from a couple of problems that make them unsuitable for people who are not experts in the respective fields: insufficient documentation, bad user interfaces, undocumented bugs, and lousy code quality (implying low reliability). I don't know GROMACS, but I certainly wouldn't use GAMESS unless I had some means of verifying its results for the exact system I am working on. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From luca@lcfs.chim.unifi.it Mon Jan 27 11:33:59 1997 Received: from cit.enscm.fr for luca@lcfs.chim.unifi.it by www.ccl.net (8.8.3/950822.1) id LAA13149; Mon, 27 Jan 1997 11:05:02 -0500 (EST) Received: from palladium.enscm.fr by cit.enscm.fr (AIX 4.1/UCB 5.64/4.03) id AA09016; Mon, 27 Jan 1997 17:02:20 +0100 Received: from uranium.enscm.fr (uranium [193.52.207.118]) by palladium.enscm.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id RAA19064; Mon, 27 Jan 1997 17:10:27 +0100 Message-Id: <32ECD30D.E79@lcfs.chim.unifi.it> Date: Mon, 27 Jan 1997 17:08:45 +0100 From: "Dr. Luca Pedocchi" Reply-To: luca@lcfs.chim.unifi.it Organization: Dipartimento di Chimica - Firenze X-Sender: "Dr. Luca Pedocchi" X-Mailer: Mozilla 4.0b1 (Win95; I) Mime-Version: 1.0 To: lrbu00@xd88.kodak.com Cc: chemistry@www.ccl.net Subject: Re: CCL:Banal Fortran Question X-Priority: Normal References: <9701270915.ZM12927@xd88.kodak.com> Content-Type: multipart/alternative; boundary="----------1BA15809278B2" ------------1BA15809278B2 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Here is an excerpt from IRIX 6.2 man f77 -backslash Treat the backslash character as a normal character instead of an escape sequence character. For example, when this is used the sequence "" will be treated as two separate characters instead of a single character. I tried just now the following code (if code can be applied ....) write(*,'(a1)')'\' write(*,'(a1)')char(92) stop end If you compile it with the option -backslash it works fine. Anyway, maybe char(92) is a more standard procedure. Luca -- Dr. Luca Pedocchi Laboratorio di Chimica Fisica delle Interfasi via Cavour, 82 - 50129 Firenze - ITALY http://lcfs.chim.unifi.it/solid/pedocchi e-mail luca@lcfs.chim.unifi.it phone +39-55-2757793 fax +39-55-219802 Non esistono uomini cattivi, se sono cucinati bene (Stefano Benni) ------------1BA15809278B2 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii

Here is an excerpt from IRIX 6.2 man f77

-backslash Treat the backslash character as a normal character instead of an escape sequence character. For example, when this is used the sequence "" will be treated as two separate characters instead of a single <TAB> character.

I tried just now the following code (if code can be applied ....)

write(*,'(a1)')'\'

write(*,'(a1)')char(92)

stop

end
If you compile it with the option -backslash it works fine. Anyway, maybe char(92) is a more standard procedure.

Luca

--

Dr. Luca Pedocchi
Laboratorio di Chimica Fisica delle Interfasi
via Cavour, 82 - 50129 Firenze - ITALY

http://lcfs.chim.unifi.it/solid/pedocchi
e-mail luca@lcfs.chim.unifi.it

phone +39-55-2757793
fax +39-55-219802

Non esistono uomini cattivi, se sono cucinati bene
(Stefano Benni)

------------1BA15809278B2-- From bruce@cosy.utmb.edu Mon Jan 27 12:19:18 1997 Received: from cosy.utmb.edu for bruce@cosy.utmb.edu by www.ccl.net (8.8.3/950822.1) id LAA13223; Mon, 27 Jan 1997 11:19:29 -0500 (EST) Received: by cosy.utmb.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id KAA07665; Mon, 27 Jan 1997 10:19:43 -0600 From: "Bruce A. Luxon" Message-Id: <9701271019.ZM7663@cosy.utmb.edu> Date: Mon, 27 Jan 1997 10:19:35 -0600 In-Reply-To: "CCL:Banal Fortran Question" (Jan 27, 9:15am) References: <9701270915.ZM12927@xd88.kodak.com> Organization: Sealy Center for Structural Biology Reply-To: bruce@nmr.utmb.edu X-Phone: (409) 747-6802 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: Subject: Re: CCL:Banal Fortran Question Cc: chemistry@www.ccl.net, McKelvey@kodakr.KODAK.COM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Be sure the backslash is escaped with another backslash. I usually put such stuff into a Hollerith but this may not always be necessary. This works: PROGRAM DUNG C CHARACTER*1 DUNG C OPEN (9,FILE='dung.out',STATUS='new',form='formatted') C DUNG = '\\' WRITE(9,'('' '' )') WRITE(9,100) DUNG, DUNG WRITE(9,'('' '')') C 100 FORMAT(5X,A1,15X,"MULTISPIN OVERHAUSER RELAXATION", 2 " ANALYSIS",11X,A1) C CLOSE(9) END Output looks like this: \ MULTISPIN OVERHAUSER RELAXATION ANALYSIS \ Bruce Luxon On Jan 27, 9:15am, wrote: > Subject: CCL:Banal Fortran Question > CCLER's: > > I am trying to write a program to take external information and feed it into > HYPERCHEM. One theing that the HYPERCHEM ".ext" file requires is that some > input lines be terminated with a \ (backslash). The "obvious" way to to write > a backslash in a format statement does not seem to work, i.e. ''\'' , does not > work as the \ is interpreted by the compiler (both on rs6000 and sgi r8000) and > gives an error. > > Any hints? > > Thanks! > > John > > -- > > John M. McKelvey email: mckelvey@Kodak.COM > Computational Science Laboratory phone: (716) 477-3335 > 2nd Floor, Bldg 83, RL > Eastman Kodak Company > Rochester, NY 14650-2216 > > -- >-- End of excerpt from -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * Sealy Center for Structural Biology U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From peon@medchem.dfh.dk Mon Jan 27 12:24:09 1997 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id LAA13324; Mon, 27 Jan 1997 11:31:41 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id RAA16307 for <@danpost.uni-c.dk:CHEMISTRY@www.ccl.net>; Mon, 27 Jan 1997 17:31:39 +0100 (MET) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id RAA02163 for ; Mon, 27 Jan 1997 17:43:42 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 27 Jan 1997 17:31:39 +0100 To: CHEMISTRY@www.ccl.net From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:basis set balance? Douglas A. Smith asked: >The question: Can people please explain the concept of having a balanced >basis set and the dangers inherent in an unbalanced set? In particular, why >can I not simply use a large basis, including extra split valance functions, >polarization and diffuse functions, only on the atoms I need them on, and a >smaller, more compact basis set on the "unimportant" atoms to my chemical >question? This would certainly save time and resources during the calculation. I'll give it a try, and hopefully I can do it in chemists language without loosing too much accuracy. The basic problem is that all basis sets are incomplete. There is no way you can use a finite number of basis functions to describe the electron density completely. You can get fairly close, but at a high cost. Now, what happens to an atom with an incomplete basis? It has some electron density that could be described better if it could use some additional basis functions. Now, if there are unused basis functions on a neighboring atom, there is always SOME way that a linear combination of those can be used to stabilize the electron density on the original atom further. Thus, the electron sharing between atoms is exaggerated and the bonds look stronger than they actually are. Now, if all atoms have very few basis functions, there aren't too many unused functions that can be used by the neighbors, so the errors (basis set deficiency and superposition errors, BSDE and BSSE) partially cancel. However, if one atom has a very small basis set and the neighbor many diffuse and polarization functions, you may get into a situation where a very substantial part of the electron density of the first atom is described by basis functions on the second. If you try to do a Mulliken analysis on such a system, you get weird results. The electron density in that region will also most probably be skewed, causing all kinds of distortions. You CAN get away with things like this, if you are careful to do only comparisons between very similar systems, where the effect stays constant. Naturally, you can get away with ANYTHING as long as you fulfill that requirement :-) Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From lrbu00@xd88.kodak.com Mon Jan 27 14:19:14 1997 Received: from kodakr.kodak.com for lrbu00@xd88.kodak.com by www.ccl.net (8.8.3/950822.1) id NAA14833; Mon, 27 Jan 1997 13:47:03 -0500 (EST) From: Received: from euler.kodak.com by kodakr.kodak.com with SMTP id AA24706 (5.67b/IDA-1.5 for <@kodakr.kodak.com:Chemistry@www.ccl.net>); Mon, 27 Jan 1997 13:45:36 -0500 Received: from xd88.kodak.com by euler.kodak.com via SMTP (940816.SGI.8.6.9/940406.SGI) for id NAA25455; Mon, 27 Jan 1997 13:46:30 -0500 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA12303; Mon, 27 Jan 1997 13:46:30 -0500 Date: Mon, 27 Jan 1997 13:46:30 -0500 Message-Id: <9701271346.ZM12813@xd88.kodak.com> X-Mailer: Z-Mail (3.0.0 15dec93) To: Chemistry@www.ccl.net Subject: Thanks re: ''\'' Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Many Thanks to all who responded concerning writing backslashes in format statements. To those who along with me who didn't know the answer, there are two approaches I received, one was to use ''\\'' instead of ''\''. This worked with 6.2 IRIX, but not with rs6k with 3.2.5. The other option suggested was to use a character filled with a data statement. Many thanks for all the suggestions! John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From kanters@urvax.urich.edu Mon Jan 27 14:30:13 1997 Received: from urvax.urich.edu for kanters@urvax.urich.edu by www.ccl.net (8.8.3/950822.1) id OAA15075; Mon, 27 Jan 1997 14:18:09 -0500 (EST) Received: from chem162.richmond.edu by urvax.urich.edu (PMDF V5.0-7 #11964) id <01IEPLBJI0M8003GWM@urvax.urich.edu>; Mon, 27 Jan 1997 14:17:57 -0500 (EST) Date: Mon, 27 Jan 1997 14:21:49 -0500 From: "Rene P.F. Kanters" Subject: Re: CCL:Quanta etc. To: D.van.der.Spoel@chem.rug.nl, Konrad Hinsen Cc: chemistry@www.ccl.net Message-id: MIME-version: 1.0 X-Mailer: Cyberdog/2.0a2 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit >In fact, of all free visualization programs I am aware of, only RasMol >works on a large range of hardware without special tricks. And while >RasMol works fine for what it was intended for, it lacks some features >that would often be useful (such as animation). > If you want animation in addition to the regular RasMol capabilities I suggest using Chime. Chime is a WWW browser plugin that works with Netscape, Cyberdog (and I understand that there are some problems with Internet Explorer). The disadvantage is that you have to create an html document that embeds the structure you want to see, but that is a small drawback. Check out http://www.mdli.com/chemscape/chime/. Rene P.F. Kanters, Ph. D. Chemistry Project Specialist Chemistry Department University of Richmond, VA 23173 phone: (804) 287-6873 www: http://www.science.urich.edu/~kanters/ From topper@cooper.edu Mon Jan 27 15:19:16 1997 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.8.3/950822.1) id OAA15299; Mon, 27 Jan 1997 14:39:25 -0500 (EST) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA21133 (5.65c/IDA-1.4.4 for ); Mon, 27 Jan 1997 14:38:40 -0500 Received: by zeus.cooper.edu id AA05423 (5.67b/IDA-1.5); Mon, 27 Jan 1997 14:35:05 -0500 From: TOPPER ROBERT Message-Id: <199701271935.AA05423@zeus.cooper.edu> Subject: Re: CCL:volume To: COMBA@akcomba.oci.uni-heidelberg.de (Peter Comba) Date: Mon, 27 Jan 1997 14:35:05 -0500 (EST) Cc: topper@cooper.edu, CHEMISTRY@www.ccl.net In-Reply-To: <20568653290@akcomba.oci.uni-heidelberg.de> from "Peter Comba" at Jan 24, 97 11:19:59 pm X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit In response to the question: > Does anyone know of an easily accessible program or have the code > (fortran or C++) and would be prepared to share it, to compute the > molecular volume from the (computed) coordinates. > Again, the Molecular Monte Carlo Home Page holds the answer! If you look at http://www.cooper.edu/engineering/chemechem/monte.html under "Software and Numerical Tools for the Discriminating Monte Carlo Practitioner" you will find a link to STERIC, a program which calulates a number of steric parameters including molecular volumes. The link takes you to ftp://hobbes.gh.wits.ac.za/pub/steric/ STERIC was contributed by Brian Craig Taverner. Best, robert ******************************************************************************** Robert Q. Topper, Chemistry Dept. email: topper@cooper.edu The Cooper Union phone: (212) 353-4378 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html Molecular Monte Carlo = http://www.cooper.edu/engineering/chemechem/monte.html ******************************************************************************** The Cooper Union, established by Peter Cooper in 1859, is a private engineering/ architecture/art college where all students receive full scholarships. ******************************************************************************** From jxh@msi.com Mon Jan 27 15:37:13 1997 Received: from bioc1.msi.com for jxh@msi.com by www.ccl.net (8.8.3/950822.1) id OAA15087; Mon, 27 Jan 1997 14:19:16 -0500 (EST) Received: from ibm12.msi.com by bioc1.msi.com via SMTP (940816.SGI.8.6.9/930416.SGI) for id LAA07465; Mon, 27 Jan 1997 11:18:48 -0800 Received: by ibm12.msi.com (AIX 3.2/UCB 5.64/4.03) id AA14497; Mon, 27 Jan 1997 11:18:41 -0800 Received: from Messages.8.5.N.CUILIB.3.45.SNAP.NOT.LINKED.ibm12.biosym.com.rs.aix3 via MS.5.6.ibm12.biosym.com.rs_aix3; Mon, 27 Jan 1997 11:18:41 -0800 (PST) Message-Id: Date: Mon, 27 Jan 1997 11:18:41 -0800 (PST) From: Joerg Hill To: CHEMISTRY@www.ccl.net Subject: Re: CCL:basis set balance? > The question: Can people please explain the concept of having a balanced > basis set and the dangers inherent in an unbalanced set? In particular, why > can I not simply use a large basis, including extra split valance functions, > polarization and diffuse functions, only on the atoms I need them on, and a > smaller, more compact basis set on the "unimportant" atoms to my chemical > question? This would certainly save time and resources during the calculation. One of the dangers of using an unbalanced basis set is that you might get electron density where it shouldn't be. If you put a good basis only where you think important things will happen and a poor basis everywhere else than the electrons which are at the atoms with the poor basis will (partially) move to the atoms with the good basis (since there is more flexibility in the basis and the total energy of the system will be lowered). So you might get the effect you were interested in, but only because you described the system the way you thought it would be. The basis set is only an approximation used to describe the electron density distribution (since there is currently no way to solve the Schroedinger equation for a larger system without this approximation). So you have to use the same quality of approximation for the whole molecule if you want to get reasonable results. Joerg-R. Hill ------------------------------------------------------------------------------- - Dr. Joerg-Ruediger Hill | Every attempt to employ mathematical methods in the Molecular Simulations | study of chemical questions must be considered pro- 9685 Scranton Road | foundly irrational and contrary to the spirit of San Diego, CA 92121-3752 | chemistry ... If mathematical analysis should ever USA | hold a prominent place in chemistry - an aberration | which is happily almost impossible - it would Phone (619) 546-5508 | occasion a rapid and widespread degeneration of Fax (619) 458-0136 | that science. E-mail jxh@msi.com | Auguste Comte, Philosophie Positive, Paris, 1838 ------------------------------------------------------------------------------- - The opinions expressed in this message are my personal opinions and no offical statements of Molecular Simulations. For informations about Molecular Simula- tions products take a look at: http://www.msi.com/. ------------------------------------------------------------------------------- - From rvenable@deimos.cber.nih.gov Mon Jan 27 16:19:16 1997 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id PAA16135; Mon, 27 Jan 1997 15:59:33 -0500 (EST) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA091677641; Mon, 27 Jan 1997 15:40:41 -0500 Date: Mon, 27 Jan 1997 15:40:41 -0500 (EST) From: Rick Venable Reply-To: Rick Venable To: "Rene P.F. Kanters" Cc: D.van.der.Spoel@chem.rug.nl, Konrad Hinsen , chemistry@www.ccl.net Subject: Re: CCL:Quanta etc. In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > >In fact, of all free visualization programs I am aware of, only RasMol > >works on a large range of hardware without special tricks. And while > >RasMol works fine for what it was intended for, it lacks some features > >that would often be useful (such as animation). Actually, with rasmol 2.6 one can make animations, by creating .ppm file output for the single frames, and combining them into an animation with mpeg_encode; the 'set write on' command was added to rasmol to allow it's use for animations, among other things. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov \/ |=| position of the FDA; for that, http://nmr1.cber.nih.gov/venable.html |=| see http://www.fda.gov ) From dsmith@CTCnet.Net Mon Jan 27 16:32:00 1997 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id PAA15878; Mon, 27 Jan 1997 15:28:43 -0500 (EST) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id PAA26741; Mon, 27 Jan 1997 15:25:01 -0500 Date: Mon, 27 Jan 1997 15:25:01 -0500 Message-Id: <199701272025.PAA26741@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: (2) basis set balance continued OK, so the real issue is BSSE and basis set flexibility for describing the space available to all electrons. For the latter, would the use of CI or multi-reference-CI help alleviate the problem? Would that be a more expensive cure than using a balanced basis? What, then, happens when one is performing calculations on systems containing both very heavy atoms and very light atoms, let's say, a lanthanide and hydrogen? If one uses an all electron basis for both atoms, isn't the basis set unbalanced? Is this at least part of the reason for effective core potentials (ECPs) -- in addition to the problem of just handling all the electrons in a reasonable time at reasonable cost? Doug -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology.