From chemistry-request@server.ccl.net Fri Jun 15 11:21:15 2001 Received: from mail.rpi.edu ([128.113.22.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5FFLF521039 for ; Fri, 15 Jun 2001 11:21:15 -0400 Received: from titanme (exothermic-04.dynamic.rpi.edu [128.113.21.159]) by mail.rpi.edu (8.11.3/8.11.3) with SMTP id f5FFLFp120586 for ; Fri, 15 Jun 2001 11:21:15 -0400 From: "Larry Lockwood" To: Subject: Classification of DATA - Easy vs Difficult Date: Fri, 15 Jun 2001 11:19:59 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 CCL'ers, I have heard mention of data set classification i.e. hard data sets to model versus easy data sets to model. I think the classification goes from 1 to 5, with 1 being the easiest and 5 being the hardest. My question is where can I find these data sets along with their classifications? I would like to test several feature selection methods on data sets ( preferably QSAR type data) of varying difficulty. In addition, I am looking for a publicly available Caco-II data set with relatively well established models for comparison. Thanks for your time. Larry Lockwood Rensselaer Polytechnic Institute Department of Chemistry From chemistry-request@server.ccl.net Fri Jun 15 11:23:38 2001 Received: from wally.uh.cu ([216.72.24.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5FFNY521136 for ; Fri, 15 Jun 2001 11:23:36 -0400 Received: from alma.uh.cu (alma.uh.cu [192.168.100.67]) by wally.uh.cu (8.11.0/8.11.0/MZ) with ESMTP id f5FFThv22978 for ; Fri, 15 Jun 2001 11:29:43 -0400 Received: from fq.uh.cu (canaria.fq.oc.uh.cu [192.168.3.4]) by alma.uh.cu (Postfix) with ESMTP id 1FB82A560F for ; Fri, 15 Jun 2001 11:27:53 -0400 (CDT) Received: from localhost (alexis@localhost) by fq.uh.cu (8.9.0/8.8.7) with SMTP id KAA11151 for ; Fri, 15 Jun 2001 10:15:22 -0400 Date: Fri, 15 Jun 2001 10:15:22 -0400 (CDT) From: Alexis Otero Calvis Reply-To: Alexis Otero Calvis To: chemistry@ccl.net Subject: LanL2DZ Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I need to know what's the efect in the result of this two input files for Gaussian. first input #T BP86/LanL2DZ opt second input #T BP86/LanL2DZ pseudo=Lanl2 opt or #T BP86/LanL2DZ pseudo=SDD opt PD: I'm not CCL member ********************************************************************* Lic. Alexis Otero Calvi Laboratorio Quimica Teorica Universidad de La Habana E-mail: alexis@fq.uh.cu (Universidad de La Habana) aotero@moa.minbas.cu (Inst.Sup. Minero Metalurgico, Moa) alexis_otero@yahoo.com (Internet) ********************************************************************* From chemistry-request@server.ccl.net Fri Jun 15 13:35:50 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5FHZo523367 for ; Fri, 15 Jun 2001 13:35:50 -0400 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id MAA03216 for ; Fri, 15 Jun 2001 12:28:47 -0500 (CDT) Date: Fri, 15 Jun 2001 12:28:47 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: SHAKE/RATTLE Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have a question regarding SHAKE. When the bond lengths are constrained by SHAKE, should the constraint force be added to the total force?. The way i have been using it is to send the new positions and previous positions and depending on the tolerance, the routine will constrain the positions. iam not computinmg the constarint forces. I have another question, how does one fix this tolerance limit? thanks!! From chemistry-request@server.ccl.net Fri Jun 15 14:18:24 2001 Received: from mailhost.msi.com ([146.202.0.242]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5FIIO524204 for ; Fri, 15 Jun 2001 14:18:24 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id LAA12381 for ; Fri, 15 Jun 2001 11:19:28 -0700 (PDT) Received: from unknown(146.202.5.50) by mailhost.msi.com via smap (V2.0) id xma012375; Fri, 15 Jun 01 11:19:19 -0700 Message-Id: <5.1.0.14.0.20010615104917.00a867f0@pop3.norton.antivirus> X-Sender: jnauss/sparky2.msi.com@pop3.norton.antivirus X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 15 Jun 2001 10:50:34 -0400 To: chemistry@ccl.net From: Jeff Nauss Subject: CHARMM: VDISTANCE keyword in NBOND options Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Within CHARMM, I came across a keyword VDISTANCE while examining some of the options for nonbonded specifications. It is used as a suggested nonbonded specification in the CHARMM27 force field as well as the Momany and Rone force field. Researching that option, I found in old c24 documentation that it is a "distance specified Van der Waal function" with no further explanation. I could not find any mention of VDISTANCE in the c27 documentation. In my tests with the option, there appears to be no effect on the calculations. Might anyone have any further information? Might it be a mere fossil or relic? Thank you in advance... -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 On June 1, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Accelrys is a subsidiary of Pharmacopeia, Inc. From chemistry-request@server.ccl.net Fri Jun 15 17:29:58 2001 Received: from franck.pc.Uni-Koeln.DE (IDENT:news@[134.95.49.83]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5FLTw511595 for ; Fri, 15 Jun 2001 17:29:58 -0400 Received: (from news@localhost) by franck.pc.Uni-Koeln.DE (8.8.7/8.8.7) id XAA19618 for CHEMISTRY@ccl.net; Fri, 15 Jun 2001 23:29:57 +0200 To: CHEMISTRY@ccl.net From: Johannes Weber Newsgroups: local.CCL Subject: SUMMARY: G98: How to calculate excited singlet states with ROHF ? Date: 15 Jun 2001 23:29:54 +0200 Organization: Physikalische Chemie Universitaet Koeln Lines: 103 Sender: weber@franck.pc.Uni-Koeln.DE Message-ID: NNTP-Posting-Host: localhost Mime-Version: 1.0 (generated by tm-edit 7.108) Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Gnus v5.6.45/XEmacs 20.4 - "Emerald" Xref: franck.pc.Uni-Koeln.DE local.CCL:8997 Dear CCL members, a few days ago I posted a question about the possibility to do restricted open shell calculations on singlet excited states with Gaussian98. Since the resonance was unexpectedly low (only two answers) I also asked a somewhat more specialized question at help@gaussian.com. Furthermore, I was asked for a summary -- here it is. Thanks to Uwe Richter, Doug Fox and David Shobe. To summarize it shortly, there is NO possibility to do RO singlet excited state calculations within Gaussian 98. (I intended to do RO DFT calculations with the B1LYP functional. Of course, there are other possibilities to handle excited singlet states). ORIGINAL POSTED MESSGAGE: ===================================================== Johannes Weber writes: > Dear CCL members, > > I have a Gaussian 98 related question: > > (How) is it possible to do calculations on excited singlet states > different from the ground state symmetry with the restricted open > shell method ? > > There is no problem with this for triplet states since there must be > at least two unpaired electrons in different MOs and one can change > these MOs by guess=alter. Alas, for the singlets the program always > seems to follow the aufbau principle resulting in a closed shell > system. Is anybody aware of a workaround? > > Thanks in advance, :-)ohannes. > > > PS: On demand I will summarize the answers. ========================================================== Answers: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1. Uwe Richter wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Johannes, ... G98 erlaubt keine ROHF-Rechnungen fuer Singuletts. Versuch's mal mit Gamess (US und UK koennen es beide). Ich glaube, mit Turbomole geht es auch. Ach so, wenn du angeregte closed-shells berechnen willst (macht nicht allzuviel Sinn, aber es geht), kannst du mit guess=alter die Orbitale so hintauschen, dass du die gewuenschte Konfiguration hast und dann scf=symm setzen, damit die Orbitale waehrend der SCF-Prozedur nicht wieder zuerueckflippen. Jaja, Molcas macht das besser. Gruss, Uwe >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2. Douglas F. Fox wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dr. Weber, The RO code is not setup for open shell singlets. There is an option in the GVB code for spin restricted open shell singlets but this is setup for HF not for DFT. The IOP(4/17) option applies to semi-empirical calculations, l402, again not DFT and the IOP(5/26) option applies to l504, which works for HF but not for DFT. The best I can suggest is to use a RB1LYP ground state with the TD option and select singlet states. It will give you vertical excitation energies not optimizations on the excited states but they will be spin restricted. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3. David Shobe wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You can use guess=alter, and pray. :-) Actually, if you can afford correlated methods, CIS does a reasonable job at finding excited states. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Comment on Davids first sentence: An extraodinary good connection to heaven seems to be necessary to perform these calculations - so I donīt have to wonder why it didnīt work for me ;-) . More seriously, only excited closed shells, i.e. excitation of an electron pair, can be calculated in this way (see Uwes mail). Regards and once again thanks to all who read the mail, :-)ohannes. ---------------------------------------------------------------------- | Johannes Weber | Email: | | Universitaet zu Koeln | Johannes.Weber@uni-koeln.de | | Institut fuer Physikalische Chemie | | | Lehrstuhl Prof. Dr. G. Hohlneicher | tel: 0049-(0)221-470-4816 | | Luxemburger Str. 116 | fax: 0049-(0)221-470-5144 | | 50939 Koeln | | ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Jun 15 20:08:14 2001 Received: from srv.cip.physik.tu-muenchen.de ([129.187.184.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5G08D513358 for ; Fri, 15 Jun 2001 20:08:13 -0400 Received: from epsilon.cip.physik.tu-muenchen.de (epsilon.cip.physik.tu-muenchen.de [129.187.184.90]) by srv.cip.physik.tu-muenchen.de (8.10.2/8.10.2) with ESMTP id f5G080P05710; Sat, 16 Jun 2001 02:08:01 +0200 (MET DST) Received: from localhost (thuber@localhost) by epsilon.cip.physik.tu-muenchen.de (8.8.6/8.8.6) with SMTP id CAA13973; Sat, 16 Jun 2001 02:08:00 +0200 (MET DST) X-Authentication-Warning: epsilon.cip.physik.tu-muenchen.de: thuber owned process doing -bs Date: Sat, 16 Jun 2001 02:08:00 +0200 (MET DST) From: Thomas Huber To: chemistry@ccl.net cc: Thomas Huber Subject: Non-pairwise summation for virials in periodic systems Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer, in the current biomolecular MD systems it is usually assumed, that the calculation of the internal virial used in pressure calculations can be only done by summation over the pairwise atomic interactions. (See Allen&Tildesley Chapter 2.4) > From the definition of this internal virial, it should be possible to calculate it just from the forces and positions of each atom. Is there any reference showing a successful application of such a non-pairwise approach in systems under periodic boundary conditions? This could possibly lead directly to a localized expression for the pressure tensor?! Yours, Thomas ----------------------------------------------------------------------------- Dr.Thomas Huber University of Arizona Tel.: (520) 621-2537 Department of Chemistry FAX: (520) 621-8407 1306 E. University Blvd. email thuber@physik.tu-muenchen.de Tucson, Arizona 85721-0041