From chemistry-request@server.ccl.net Thu Mar 7 04:18:27 2002 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g279IQ529790 for ; Thu, 7 Mar 2002 04:18:26 -0500 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id KAA25796 for ; Thu, 7 Mar 2002 10:17:53 +0100 (MET) Date: Thu, 7 Mar 2002 10:17:53 +0100 (MET) Message-Id: <200203070917.KAA25796@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: TDDFT in terms of polarization propagator Hi, Does someone know whether TDDFT (or TDDFRT) has been derived in terms of the polarization propagator (Green's functions). It would easen the comparison with standard derivation of RPA (or TDHF). Thanks, Serge Kwasniewski ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Thu Mar 7 02:02:52 2002 Received: from mail0.epfl.ch ([128.178.50.57]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2772p524489 for ; Thu, 7 Mar 2002 02:02:51 -0500 Received: (qmail 27526 invoked from network); 7 Mar 2002 07:02:18 -0000 Received: from icmbpc029.epfl.ch (HELO icmbpc029) (128.178.55.30) by mail0.epfl.ch with SMTP; 7 Mar 2002 07:02:18 -0000 Message-ID: X-Mailer: XFMail 1.4.0 on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit MIME-Version: 1.0 In-Reply-To: Date: Thu, 07 Mar 2002 08:02:18 +0100 (MET) Sender: aborel@icmbpc029 From: Alain Borel To: Jim Phillips Subject: RE: CCL:video cards for RedHat 7.2 Cc: chemistry@ccl.net, Donald Keidel On 07-Mar-02 Jim Phillips wrote: > Hi, > > See http://www.ks.uiuc.edu/Research/vmd/current/accelerators.html > > For real 3D acceration under Linux you want an NVidia GeForce something. Unless you prefere open-source drivers, in which case you'll choose Matrox or ATI. Nvidia provide their own binary-only driver. Alain Borel Institute of Molecular and Biological Chemistry Swiss Federal Institute of Technology - Lausanne -- Alain Borel From chemistry-request@server.ccl.net Thu Mar 7 09:09:30 2002 Received: from mail.iq.ufrj.br ([146.164.3.137]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g27E9T503787 for ; Thu, 7 Mar 2002 09:09:29 -0500 Received: from nahy (pxq92.iq.ufrj.br [146.164.6.92]) by mail.iq.ufrj.br (Postfix) with SMTP id 50D093F55 for ; Thu, 7 Mar 2002 11:05:30 -0300 (BRT) Message-ID: <004d01c1c5e2$0cf8d780$5c06a492@iq.ufrj.br> From: "Daniel L. Bhering" To: Subject: MNDO Curvilinear step convergence Date: Thu, 7 Mar 2002 11:12:00 -0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_004A_01C1C5C8.E73F4920" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_004A_01C1C5C8.E73F4920 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Friends, I have some problems with semiempirical calculations (MNDO) under = Gaussian 98 of system with 170 atoms (Si,Al, O and H). Some constrains = are used in order to fix the geometry like in zeolite cell (the H atoms = are frozen using addredundant option). The message error is:=20 =20 Curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in d:\quimica\g98w\l103.exe. Job cpu time: 0 days 0 hours 10 minutes 5.0 seconds. File lengths (MBytes): RWF=3D 33 Int=3D 0 D2E=3D 0 Chk=3D 36 Scr=3D 1 I would like to know if it is possible to change the Curvilinear step = convergence or increase its maximum step. Thanks in advance, Daniel L. Bhering =20 The end of the file is: = GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Use GDIIS/GDPIS optimizer. Internal Forces: Max 0.066574391 RMS 0.005245074 Search for a local minimum. Step number 2 out of a maximum of 927 All quantities printed in internal units (Hartrees-Bohrs-Radians) Swaping is turned off. 2 1 -0.1092465E-02 0.2080001E-02 0.5252233=20 Update second derivatives using information from points 1 2 Trust test=3D 1.72D+00 RLast=3D 1.33D-01 DXMaxT set to 3.98D-01 lowest eigenvalue of the Hessian is 0.1457 . RFO step: Lambda=3D 2.16960443D-04. DIIS coeff's: 5.10805 -4.10805 Cosine: 0.998 > 0.866 Length: 1.064 GDIIS step was calculated using 2 of the last 2 vectors. Iteration 1 RMS(Cart)=3D 0.05470182 RMS(Int)=3D 0.00156511 Iteration 2 RMS(Cart)=3D 0.00463266 RMS(Int)=3D 0.00054886 Iteration 3 RMS(Cart)=3D 0.00001324 RMS(Int)=3D 0.00054881 . . . Iteration 97 RMS(Cart)=3D 0.00000239 RMS(Int)=3D 0.00016218 Iteration 98 RMS(Cart)=3D 0.00000234 RMS(Int)=3D 0.00016243 Iteration 99 RMS(Cart)=3D 0.00000229 RMS(Int)=3D 0.00016268 Iteration100 RMS(Cart)=3D 0.00000224 RMS(Int)=3D 0.00016293 Curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in d:\quimica\g98w\l103.exe. Job cpu time: 0 days 0 hours 10 minutes 5.0 seconds. File lengths (MBytes): RWF=3D 33 Int=3D 0 D2E=3D 0 Chk=3D 36 Scr=3D 1 ------=_NextPart_000_004A_01C1C5C8.E73F4920 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Friends,
I have some problems with semiempirical = calculations (MNDO) under Gaussian 98 of system with 170 atoms (Si,Al, O = and H).=20 Some constrains are used in order to fix the geometry like in zeolite = cell (the=20 H atoms are frozen using addredundant option).
The message = error is: 
  
Curvilinear step not converged.
Error imposing constraints
Error termination via Lnk1e in d:\quimica\g98w\l103.exe.
Job cpu time: 0 days 0 hours 10 minutes 5.0 seconds.
File lengths (MBytes): RWF=3D 33 Int=3D 0 D2E=3D 0 Chk=3D 36 Scr=3D = 1
 
I would like to know if it is possible = to change=20 the Curvilinear step convergence = or=20 increase its maximum step.
 
 
Thanks in advance,
 
Daniel L. Bhering
 
 
The end of the file is:
 
=
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG= rad
Berny optimization.
Use GDIIS/GDPIS optimizer.
Internal Forces: Max 0.066574391 RMS 0.005245074
Search for a local minimum.
Step number 2 out of a maximum of 927
All quantities printed in internal units = (Hartrees-Bohrs-Radians)
Swaping is turned off.
2 1 -0.1092465E-02 0.2080001E-02 0.5252233
Update second derivatives using information from points 1 2
Trust test=3D 1.72D+00 RLast=3D 1.33D-01 DXMaxT set to = 3.98D-01
lowest eigenvalue of the Hessian is 0.1457 .
RFO step: Lambda=3D 2.16960443D-04.
DIIS coeff's: 5.10805 -4.10805
Cosine: 0.998 > 0.866
Length: 1.064
GDIIS step was calculated using 2 of the last 2 vectors.
Iteration 1 RMS(Cart)=3D 0.05470182 RMS(Int)=3D 0.00156511
Iteration 2 RMS(Cart)=3D 0.00463266 RMS(Int)=3D 0.00054886
Iteration 3 RMS(Cart)=3D 0.00001324 RMS(Int)=3D 0.00054881
.
.
.
 
 
Iteration 97 RMS(Cart)=3D 0.00000239 RMS(Int)=3D 0.00016218
Iteration 98 RMS(Cart)=3D 0.00000234 RMS(Int)=3D 0.00016243
Iteration 99 RMS(Cart)=3D 0.00000229 RMS(Int)=3D 0.00016268
Iteration100 RMS(Cart)=3D 0.00000224 RMS(Int)=3D 0.00016293
Curvilinear step not converged.
Error imposing constraints
Error termination via Lnk1e in d:\quimica\g98w\l103.exe.
Job cpu time: 0 days 0 hours 10 minutes 5.0 seconds.
File lengths (MBytes): RWF=3D 33 Int=3D 0 D2E=3D 0 Chk=3D 36 = Scr=3D=20 1
------=_NextPart_000_004A_01C1C5C8.E73F4920-- From chemistry-request@server.ccl.net Thu Mar 7 11:17:20 2002 Received: from mail.uh.edu ([129.7.69.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g27GHK506462 for ; Thu, 7 Mar 2002 11:17:20 -0500 Received: from conversion-daemon by mail.uh.edu (Sun Internet Mail Server sims.4.0.2000.10.12.16.25.p8) id <0GSM00C012JYFQ@mail.uh.edu> for chemistry@ccl.net; Thu, 7 Mar 2002 10:16:46 -0600 (CST) Received: from uh.edu (129-7-239-221.dhcp.uh.edu [129.7.239.221]) by mail.uh.edu (Sun Internet Mail Server sims.4.0.2000.10.12.16.25.p8) with ESMTP id <0GSM00AQG2JXXU@mail.uh.edu>; Thu, 07 Mar 2002 10:16:45 -0600 (CST) Date: Thu, 07 Mar 2002 10:09:47 -0600 From: Joe Huang Subject: Re: CCL:video cards for RedHat 7.2 To: Donald Keidel Cc: chemistry@ccl.net Message-id: <3C8790CB.70401@uh.edu> MIME-version: 1.0 Content-type: MULTIPART/ALTERNATIVE; BOUNDARY="Boundary_(ID_bLYgeYdMn1T3Wfso6xTajA)" X-Accept-Language: en,pdf User-Agent: Mozilla/5.0 (Windows; U; WinNT4.0; en-US; rv:0.9.1) Gecko/20010607 Netscape6/6.1b1 References: <004501c1c55d$221b00f0$529c178a@dopetec> --Boundary_(ID_bLYgeYdMn1T3Wfso6xTajA) Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7BIT Hi there, The Nvidia GeForce4 models just come out and it costs about $120 US dollars for a model with 64 MB DDR memory. This will be a good choice! Joe -- Donald Keidel wrote: > Hello all, > > > > I am thinking of buying a new video card for my redhat linux 7.2 and > windows 2000 dual boot system. I need to limit the card type to 2x > AGP. I am wondering if anyone can recommend a good video card. I > know I can look at the hardware compatibility lists, but I want to > know what CCLers feel are good graphics cards when considering the > needs of the software we use. Thanks for any help. > > > > Don > > --------------------------------------------------- > Donald J. Keidel > University of California, Riverside > Department of Biochemistry and Molecular Biology > Riverside, CA 92521 > phone: (909) 787-5493 > fax: (909) 787-4434 > dkeidel397@att.net > webpage: > www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm > > --Boundary_(ID_bLYgeYdMn1T3Wfso6xTajA) Content-type: text/html; charset=us-ascii Content-transfer-encoding: 7BIT Hi there,
The Nvidia GeForce4 models just come out and it costs about $120 US dollars for a model with 64 MB DDR memory.
This will be a good choice!

Joe
--

Donald Keidel wrote:
Hello all,
 
I am thinking of buying a new video card for my redhat linux 7.2 and windows 2000 dual boot system.  I need to limit the card type to 2x AGP.  I am wondering if anyone can recommend a good video card.  I know I can look at the hardware compatibility lists, but I want to know what CCLers feel are good graphics cards when considering the needs of the software we use.  Thanks for any help.
 
Don
---------------------------------------------------
Donald J. Keidel
University of California, Riverside
Department of Biochemistry and Molecular Biology
Riverside, CA 92521
phone:  (909) 787-5493
fax:  (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm

--Boundary_(ID_bLYgeYdMn1T3Wfso6xTajA)-- From chemistry-request@server.ccl.net Thu Mar 7 11:18:52 2002 Received: from umbi3.umbi.umd.edu ([136.160.7.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g27GIq506520 for ; Thu, 7 Mar 2002 11:18:52 -0500 Received: from umbi.umd.edu (hatter.carb.nist.gov [129.6.113.76]) by umbi3.umbi.umd.edu (Netscape Messaging Server 4.15) with ESMTP id GSM2NO00.25M for ; Thu, 7 Mar 2002 11:19:00 -0500 Message-ID: <3C8792DA.F1B5E230@umbi.umd.edu> Date: Thu, 07 Mar 2002 11:18:34 -0500 From: "Michael K. Gilson" X-Mailer: Mozilla 4.78 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: turning chemical names into connection tables Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, In order to speed data entry on drug-like compounds into BindingDB (www.bindingdb.org), we need a quick method of going from something like "R1=N-(Methylcarbamoyl)methyl" to a molfile or smiles string. I'd appreciate advice on available software --commercial or academic -- to help with this. Thanks, Mike From chemistry-request@server.ccl.net Thu Mar 7 10:17:09 2002 Received: from cytosine.cgl.ucsf.edu ([128.218.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g27FH9505230 for ; Thu, 7 Mar 2002 10:17:09 -0500 Received: from cytosine.cgl.ucsf.edu (socrates.cgl.ucsf.edu [128.218.27.3]) by cytosine.cgl.ucsf.edu (8.12.2/8.12.2/GSC1.13) with ESMTP id g27FGbPX1185996; Thu, 7 Mar 2002 07:16:37 -0800 (PST) Message-Id: <200203071516.g27FGbPX1185996@cytosine.cgl.ucsf.edu> To: Alain Borel cc: Jim Phillips , chemistry@ccl.net, Donald Keidel , dek@cgl.ucsf.EDU Subject: Re: CCL:video cards for RedHat 7.2 In-Reply-To: Your message of "Thu, 07 Mar 2002 08:02:18 +0100." Date: Thu, 07 Mar 2002 07:16:37 -0800 From: "David Konerding, Ph.D." Alain Borel writes: > >On 07-Mar-02 Jim Phillips wrote: >> Hi, >> >> See http://www.ks.uiuc.edu/Research/vmd/current/accelerators.html >> >> For real 3D acceration under Linux you want an NVidia GeForce something. > >Unless you prefere open-source drivers, in which case you'll choose Matrox >or ATI. Nvidia provide their own binary-only driver. Neither open source driver provides reasonable hardware acceleration for transformation and lighting, which is critical when modeling large structures. The ATI driver has been trying to add this for some time, but I don't believe it was ever achieved. I don't have any problem with closed source drivers as long as they integrate well into my system and don't cause a problem when I upgrade to new kernels, etc. My personal favorite video card on Linux is the ATI FireGL2, which has very good performance, a "reasonable" price, closed source driver from ATI, and mostly importantly to me, support for quad buffered stereo on Linux. I have tested this card with Chimera and it works wonderfully, even in situations where I am looking at very large structures (1jj2, 99000 atoms) with smooth ribbons and surfaces. I also have a GeForce2 MX at home, which I've tested using the nvidia drivers and it works pretty well- good enough to model moderately large structures with no visual delay. No card w/o HW T&L support can do this, even with a fast CPU (and I want to leave my CPU for other tasks). Dave From chemistry-request@server.ccl.net Thu Mar 7 11:53:40 2002 Received: (from ccl@localhost) by server.ccl.net (8.11.6/8.11.0) id g27GreO07449; Thu, 7 Mar 2002 11:53:40 -0500 From: "Peter Lykos" To: Subject: 02.08.22 ACS Boston: COMP: Symposium: The Chemistry Of Computers Date: Thu, 7 Mar 2002 10:34:25 -0800 Message-ID: Symposium, The Chemistry Of Computers, sponsored by the ACS Division of Computers in Chemistry, COMP, at the 18-22 August 2002 Natl Mtg of the AmChemSoc in Boston The AmChemSoc Division of Computers in Chemistry, COMP, has a new initiative; namely, The Chemistry Of Computers. Thus COMP is reaching out beyond algorithms and programming to the Chemistry underlying the stuff of which computers are made and associated technologies. As these devices become more and more compact we need to understand better what more is possible working at the level of molecular science. Of course that includes micro and molecular level electronics, as well as self-assembly of intelligent devices, but ranges further into the Chemistry of displays, telecommunication materials, the computer-human interface, and beyond. Chemists are becoming computer engineers. Potential contributors to this COMP Symposium, The Chemistry OF Computers, should contact the Symposium Organizer, IIT Professor Peter Lykos ( lykos@iit.edu ). Titles and abstracts may be submitted by 25 March 2002, http://oasys.acs.org/oasys.htm . Please spread the word. From chemistry-request@server.ccl.net Thu Mar 7 12:23:33 2002 Received: from [172.17.1.4] ([198.112.109.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g27HNW508367 for ; Thu, 7 Mar 2002 12:23:33 -0500 Received: from 172.16.1.10 by 172.17.1.4 with SMTP (QuickMail Pro Server for MacOS 1.0.3); 07 MAR 02 12:22:51 UT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: jsb@mail.cambridgesoft.com Message-Id: In-Reply-To: <3C8792DA.F1B5E230@umbi.umd.edu> Date: Thu, 7 Mar 2002 12:22:48 -0500 To: "Michael K. Gilson" From: Jonathan Brecher Subject: Re: CCL:turning chemical names into connection tables Cc: chemistry@ccl.net >In order to speed data entry on drug-like compounds into BindingDB >(www.bindingdb.org), we need a quick method of going from something like >"R1=N-(Methylcarbamoyl)methyl" to a molfile or smiles string. I'd >appreciate advice on available software --commercial or academic -- >to help with this. ChemDraw Ultra will do this (assuming you can preprocess to remove the "R1=" part, and leave just the actual name string). Note that that specific example likely has a typo. It's probably intended to be "(N-methylcarbamoyl)methyl" Jonathan Brecher CambridgeSoft Corporation jsb@cambridgesoft.com