From chemistry-request@server.ccl.net Thu Nov 14 02:32:43 2002 Received: from bh.knu.ac.kr ([155.230.10.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAE7WfD21230 for ; Thu, 14 Nov 2002 02:32:42 -0500 Received: from bh.kyungpook.ac.kr (bh [155.230.10.2]) by bh.knu.ac.kr (8.11.6+Sun/8.11.2) with SMTP id gAE7Om522686 for ; Thu, 14 Nov 2002 16:24:48 +0900 (KST) Received: from cchoi (p181_53.kyungpook.ac.kr [155.230.181.53]) by bh.kyungpook.ac.kr with SMTP (MailShield v2.04 - SOLARIS/SPARC Jul 18 2001 17:16:48); Thu, 14 Nov 2002 16:24:48 +0900 From: "Cheol Ho Choi" To: Subject: Cannot mix post-SCF and DFT ? Date: Thu, 14 Nov 2002 16:32:41 +0900 Message-ID: <004101c28bb0$03be8e00$35b5e69b@cchoi> MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4024 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear CCLers, Does anybody know what the meanig of the following Gaussian error message? Cannot mix post-SCF and DFT I'm getting this from time-dependent calculations. Thanks in advance Cheol From chemistry-request@server.ccl.net Thu Nov 14 04:08:12 2002 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAE98BD23976 for ; Thu, 14 Nov 2002 04:08:11 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id B20979167; Thu, 14 Nov 2002 10:08:10 +0100 (CET) To: gamess-l@gl.ciw.edu, chemistry@ccl.net Subject: GAMESS: pgi compilation Message-ID: <1037264890.3dd367faa297c@webmail.u-picardie.fr> Date: Thu, 14 Nov 2002 10:08:10 +0100 (CET) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, I just finished to compile the last GAMESS version on Debian 2.2 with either g77 or pgf77. (For pgf77 we had to modify the ddisoc.c file as it is described in the source file) If I run the 32 tests with the binary obtained from g77, all finished "gracefully". On the contrary, with the binary built with pgf77, the input number 19 stays blocked... See below: nautilus1:~/link/gamess> tail exam19.log 2-EL. CONTRIBUTION(CM-1) 0.0000 -49.4168I < 1-1A1 (MS= 0.0)|HSO| 1-3A2 (MS= 1.0)> = 0.0000 0.0000I [Z] 1-EL. CONTRIBUTION(CM-1) 0.0000 0.0000I 2-EL. CONTRIBUTION(CM-1) 0.0000 0.0000I < 1-1A1 (MS= 0.0)|HSO| 1-3A2 (MS=-1.0)> = 0.0000 0.0000I [P] 1-EL. CONTRIBUTION(CM-1) 0.0000 0.0000I 2-EL. CONTRIBUTION(CM-1) 0.0000 0.0000I STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.1 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 107.69% Is it a known problem ? Thanks, Kind regards, Francois From chemistry-request@server.ccl.net Thu Nov 14 04:23:21 2002 Received: from cclh41.chm.tu-dresden.de ([141.30.198.41]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAE9NLD24775 for ; Thu, 14 Nov 2002 04:23:21 -0500 Received: from cclh41 (localhost [127.0.0.1]) by cclh41.chm.tu-dresden.de (8.11.3/8.11.3/SuSE Linux 8.11.1-0.5) with SMTP id gAE9MrB03229 for ; Thu, 14 Nov 2002 10:22:53 +0100 Content-Type: text/plain; charset="iso-8859-1" From: Matthias Mann Reply-To: Matthias.Mann@chemie.tu-dresden.de Organization: TU Dresden To: Chemistry@ccl.net Subject: Re: CCL:GAMESS: pgi compilation Date: Thu, 14 Nov 2002 10:22:53 +0100 X-Mailer: KMail [version 1.2] References: <1037264890.3dd367faa297c@webmail.u-picardie.fr> In-Reply-To: <1037264890.3dd367faa297c@webmail.u-picardie.fr> MIME-Version: 1.0 Message-Id: <02111410225302.03183@cclh41> Content-Transfer-Encoding: 8bit Hallo Francois, some weeks ago I wrote to the Gamess list (maybe this helps): ... Furthermore, there was once more the exam19 problem because of optimizing the code with -O2 in zheev, as observed earlier (see http://www.chm.tu-dresden.de/edv/gamess99/comp.html ). So at the end the according lines in "comp" for pgf77 (ver. 3.2) looks like: if ($TARGET == linux-pc) then setenv PATH $PATH\:/home/apps/pgi/linux86/bin setenv PGI /home/apps/pgi if (($MODULE == qfmm) || ($MODULE == solib) || ($MODULE == zheev)) then mv $MODULE.f $MODULE.junk sed -e s/DREAL/DBLE/g $MODULE.junk > $MODULE.f rm -f $MODULE.junk endif set OPT = '-O2 -Msecond_underscore' if ($MODULE == zheev) set OPT = '-O0 -Msecond_underscore' set echo pgf77 -c $OPT $MODULE.f unset echo endif On Thursday 14 November 2002 10:08, you wrote: > Dear All, > > I just finished to compile the last GAMESS version on Debian 2.2 with > either g77 or pgf77. (For pgf77 we had to modify the ddisoc.c file as it is > described in the source file) > > If I run the 32 tests with the binary obtained from g77, all finished > "gracefully". On the contrary, with the binary built with pgf77, the input > number 19 stays blocked... See below: > > nautilus1:~/link/gamess> tail exam19.log > 2-EL. CONTRIBUTION(CM-1) 0.0000 -49.4168I > < 1-1A1 (MS= 0.0)|HSO| 1-3A2 (MS= 1.0)> = 0.0000 0.0000I > [Z] 1-EL. CONTRIBUTION(CM-1) 0.0000 0.0000I > 2-EL. CONTRIBUTION(CM-1) 0.0000 0.0000I > < 1-1A1 (MS= 0.0)|HSO| 1-3A2 (MS=-1.0)> = 0.0000 0.0000I > [P] 1-EL. CONTRIBUTION(CM-1) 0.0000 0.0000I > 2-EL. CONTRIBUTION(CM-1) 0.0000 0.0000I > > STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.1 ( 0.0 MIN) > TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 107.69% > > Is it a known problem ? > > Thanks, Kind regards, Francois > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net -- Dr. Matthias Mann Fachrichtung Chemie, TU Dresden, D-01062 Dresden Tel./Fax: +49 (351) 463-34286 Email: Matthias.Mann@chemie.tu-dresden.de From chemistry-request@server.ccl.net Thu Nov 14 06:55:00 2002 Received: from uscmail.usc.es ([193.144.75.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAEBsxD28337 for ; Thu, 14 Nov 2002 06:54:59 -0500 Received: from antonio (priv120.usc.es [193.144.74.118]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id MAA16977 for ; Thu, 14 Nov 2002 12:54:57 +0100 (MET) Content-Type: text/plain; charset="iso-8859-1" From: Antonio Fernandez Reply-To: qftramos@usc.es To: "CCL" Subject: Error in GAMESS Date: Thu, 14 Nov 2002 13:55:50 -0500 X-Mailer: KMail [version 1.2] MIME-Version: 1.0 Message-Id: <02111413555000.01748@antonio> Content-Transfer-Encoding: 8bit Hi everybody, Does anybody know the meaning of the following GAMESS US 2002 for Linux? *** ERROR *** ATTEMPT TO READ A DAF RECORD THAT WAS NEVER WRITTEN. RECORD NUMBER 20 OF LENGTH 2628 DOES NOT EXIST. CHECK -PROG.DOC- FOR A LIST OF DIRECT ACCESS FILE CONTENTS EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Wed Nov 13 23:06:34 2002 Thanks in advance, -- Antonio Fernandez Ramos Dpto de Quimica Fisica Facultade de Quimica Universidade de Santiago de Compostela 15706 Santiago de Compostela Spain E-mail: qftramos@usc.es Phone:(+34)981563100 Ext:14450 Fax:(+34)981595012 http://qfbaco.usc.es/bindex.html From chemistry-request@server.ccl.net Thu Nov 14 02:32:43 2002 Received: from nomina.net.lu.se ([130.235.132.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAE7WgD21232 for ; Thu, 14 Nov 2002 02:32:42 -0500 Received: from csxp (CS-XP1800.mig.lu.se [130.235.104.90]) by nomina.net.lu.se (8.9.3/8.9.0) with SMTP id IAA14211 for ; Thu, 14 Nov 2002 08:33:10 +0100 (MET) Message-ID: <000a01c28bb0$6c818e10$5a68eb82@csxp> From: =?iso-8859-1?Q?Emanuel_Bj=F6rne?= To: Subject: Ligand centroid and ligand torsional angles in AutoDock Date: Thu, 14 Nov 2002 08:35:36 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C28BB8.CE1D5F70" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C28BB8.CE1D5F70 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi! How is the centroid of a ligand defined in AutoDock3.0? And what = torsional angles are possible for the ligand to have? Staggered and = eclipsed or are they totally free to set at any angle between -180 and = 180 degrees? Thanks. Emanuel ------=_NextPart_000_0007_01C28BB8.CE1D5F70 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi!

How=20 is the centroid of a ligand defined in AutoDock3.0? And what torsional = angles=20 are possible for the ligand to have? Staggered and eclipsed or are they = totally=20 free to set at any angle between -180 and 180=20 degrees?

Thanks.

Emanuel
------=_NextPart_000_0007_01C28BB8.CE1D5F70-- From chemistry-request@server.ccl.net Wed Nov 13 22:44:04 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAE3i3D16944 for ; Wed, 13 Nov 2002 22:44:03 -0500 Received: from cwlaptop (syr-24-58-38-139.twcny.rr.com [24.58.38.139]) by cornell.edu (8.9.3/8.9.3) with SMTP id WAA22254 for ; Wed, 13 Nov 2002 22:44:02 -0500 (EST) Message-ID: <000e01c28b90$2132bd00$6500a8c0@cwlaptop> From: "Connie Chang" To: Subject: Question about how the SCF Energy converges in Gaussian98 Date: Wed, 13 Nov 2002 22:44:26 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000B_01C28B66.37FC6C90" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_000B_01C28B66.37FC6C90 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi everyone -- I'm sorry about clogging up everyone's mailboxes again. But I have yet = another question about the SCF convergence with my molecule (~100 = atoms). As I mentioned previously, I was able to find the optimized = structure for the neutral case without a problem, but am having a lot of = trouble with the charged (-1) case. I tried many of your wonderful = suggestions -- such as level shifting, using the Guess=3Dread option = where I used the checkpoint file for the successful, neutral case, using = SCF=3Dqc and changing the max number of steps to a higher number. =20 I'm now able to get Gaussian to converge the SCF energy once. Although = how it does so is mysterious to me. This is the output: It=3D668 PL=3D 1.00D-01 DiagD=3DFF ESCF=3D 1458.118125 Diff=3D = 3.34D+01 RMSDP=3D 6.02D-03. It=3D669 PL=3D 8.69D-02 DiagD=3DFF ESCF=3D 1269.316938 = Diff=3D-1.89D+01 RMSDP=3D 9.23D-03. It=3D670 PL=3D 1.04D-01 DiagD=3DFF ESCF=3D 1062.608204 = Diff=3D-2.07D+01 RMSDP=3D 8.57D-03. It=3D671 PL=3D 7.02D-02 DiagD=3DFF ESCF=3D 1325.914799 Diff=3D = 2.63D+01 RMSDP=3D 6.15D-03. It=3D672 PL=3D 8.38D-02 DiagD=3DFF ESCF=3D 1685.927152 Diff=3D = 3.60D+01 RMSDP=3D 1.08D-02. It=3D673 PL=3D 1.14D-01 DiagD=3DFF ESCF=3D 1299.512442 = Diff=3D-3.86D+01 RMSDP=3D 9.21D-03. It=3D674 PL=3D 9.54D-02 DiagD=3DFF ESCF=3D 1241.061125 = Diff=3D-5.85D+00 RMSDP=3D 5.78D-03. It=3D675 PL=3D 8.09D-02 DiagD=3DFF ESCF=3D 1278.716278 Diff=3D = 3.77D+00 RMSDP=3D 9.87D-03. It=3D676 PL=3D 9.82D-02 DiagD=3DFF ESCF=3D 1361.857650 Diff=3D = 8.31D+00 RMSDP=3D 9.23D-03. It=3D677 PL=3D 1.29D-01 DiagD=3DFF ESCF=3D 1536.868164 Diff=3D = 1.75D+01 RMSDP=3D 6.07D-03. It=3D678 PL=3D 6.85D-02 DiagD=3DFF ESCF=3D 1271.661599 = Diff=3D-2.65D+01 RMSDP=3D 9.45D-03. It=3D679 PL=3D 7.64D-02 DiagD=3DFF ESCF=3D 929.155505 = Diff=3D-3.43D+01 RMSDP=3D 8.54D-03. It=3D680 PL=3D 1.07D-01 DiagD=3DFF ESCF=3D 1485.405483 Diff=3D = 5.56D+01 RMSDP=3D 6.20D-03. It=3D681 PL=3D 8.53D-02 DiagD=3DFF ESCF=3D 1551.560355 Diff=3D = 6.62D+00 RMSDP=3D 9.85D-03. It=3D682 PL=3D 8.91D-02 DiagD=3DFF ESCF=3D 1008.530183 = Diff=3D-5.43D+01 RMSDP=3D 8.72D-03. It=3D683 PL=3D 8.29D-02 DiagD=3DFF ESCF=3D 1254.460730 Diff=3D = 2.46D+01 RMSDP=3D 5.82D-03. It=3D684 PL=3D 9.05D-02 DiagD=3DFF ESCF=3D 1373.782809 Diff=3D = 1.19D+01 RMSDP=3D 9.83D-03. It=3D685 PL=3D 8.17D-02 DiagD=3DFF ESCF=3D 1067.847535 = Diff=3D-3.06D+01 RMSDP=3D 9.15D-03. It=3D686 PL=3D 7.68D-02 DiagD=3DFF ESCF=3D 1398.571380 Diff=3D = 3.31D+01 RMSDP=3D 6.08D-03. It=3D687 PL=3D 9.61D-02 DiagD=3DFF ESCF=3D 1666.016422 Diff=3D = 2.67D+01 RMSDP=3D 1.09D-02. It=3D688 PL=3D 9.80D-02 DiagD=3DFF ESCF=3D 1357.094370 = Diff=3D-3.09D+01 RMSDP=3D 9.29D-03. It=3D689 PL=3D 5.77D-02 DiagD=3DFF ESCF=3D 1270.824001 = Diff=3D-8.63D+00 RMSDP=3D 5.86D-03. It=3D690 PL=3D 6.98D-02 DiagD=3DFF ESCF=3D 1391.204663 Diff=3D = 1.20D+01 RMSDP=3D 9.97D-03. ALL CONVERGERS ARE NOW FORCED ON SHIFT=3D1000, PULAY ON, CAMP-KING ON AND ITERATION COUNTER RESET It=3D 1 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D -41220.458895 = Diff=3D-4.13D+03 RMSDP=3D 9.97D-03. It=3D 2 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 1627.826035 Diff=3D = 4.28D+03 RMSDP=3D 9.97D-03. It=3D 3 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 1554.928765 = Diff=3D-7.29D+00 RMSDP=3D 9.97D-03. It=3D 4 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 1457.010912 = Diff=3D-9.79D+00 RMSDP=3D 9.97D-03. It=3D 4 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 1311.192626 = Diff=3D-9.79D+00 RMSDP=3D 9.97D-03. It=3D 4 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 1127.086921 = Diff=3D-9.79D+00 RMSDP=3D 9.97D-03. It=3D 4 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 992.289552 = Diff=3D-9.79D+00 RMSDP=3D 9.97D-03. It=3D 4 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 821.787194 = Diff=3D-9.79D+00 RMSDP=3D 9.97D-03. It=3D 4 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 840.269011 = Diff=3D-9.79D+00 RMSDP=3D 9.97D-03. It=3D 4 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 800.888717 = Diff=3D-9.79D+00 RMSDP=3D 9.97D-03. It=3D 5 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 780.249572 = Diff=3D-6.77D+01 RMSDP=3D 9.97D-03. It=3D 5 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 730.748452 = Diff=3D-6.77D+01 RMSDP=3D 9.97D-03. It=3D 5 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 778.807603 = Diff=3D-6.77D+01 RMSDP=3D 9.97D-03. It=3D 5 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 708.473922 = Diff=3D-6.77D+01 RMSDP=3D 9.97D-03. It=3D 6 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 706.453896 = Diff=3D-7.38D+00 RMSDP=3D 9.97D-03. It=3D 6 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 700.609511 = Diff=3D-7.38D+00 RMSDP=3D 9.97D-03. It=3D 6 PL=3D 3.95D-02 DiagD=3DTT ESCF=3D 707.578870 = Diff=3D-7.38D+00 RMSDP=3D 9.97D-03. It=3D 6 PL=3D 3.84D-05 DiagD=3DTT ESCF=3D 700.075476 = Diff=3D-7.38D+00 RMSDP=3D 9.97D-03. It=3D 6 PL=3D 3.84D-05 DiagD=3DTT ESCF=3D 697.862649 = Diff=3D-7.38D+00 RMSDP=3D 9.97D-03. It=3D 6 PL=3D 3.84D-05 DiagD=3DTT ESCF=3D 696.972832 = Diff=3D-7.38D+00 RMSDP=3D 9.97D-03. It=3D 6 PL=3D 3.84D-05 DiagD=3DTT ESCF=3D 697.097586 = Diff=3D-7.38D+00 RMSDP=3D 9.97D-03. It=3D 7 PL=3D 3.84D-05 DiagD=3DTT ESCF=3D 696.168985 = Diff=3D-1.03D+00 RMSDP=3D 9.97D-03. As you can see, the first 600+ iterations, the ESCF oscillates, but = after the ALL CONVERGERS ARE NOW FORCED ON SHIFT=3D1000, PULAY ON, = CAMP-KING ON AND ITERATION COUNTER RESET it seems to settle down and eventually converges. However, then it does = a geometric optimization step, and the ESCF no longer converges. It = oscillates until I finally get the UNABLE TO ACHIEVE SELF-CONSISTENCE = error... First, what is this ALL CONVERGES ARE NOW FORCED ON SHIFT=3D1000.... = step? And secondly, why when Gaussian has moved the atoms a little bit to do = the geometric optimization part, does the SCF convergence become = problematic again? =20 I'm not progressing very far in this calculation and I am very perplexed = at what to do next. Can someone tell me what I am doing wrong? Thank you, Connie ------=_NextPart_000_000B_01C28B66.37FC6C90 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi everyone --
 
I'm sorry about clogging up everyone's = mailboxes=20 again.  But I have yet another question about the SCF convergence = with my=20 molecule (~100 atoms).  As I mentioned previously, I was able to = find the=20 optimized structure for the neutral case without a problem, but am = having a lot=20 of trouble with the charged (-1) case.  I tried many of your = wonderful=20 suggestions -- such as level shifting, using the Guess=3Dread option = where I used=20 the checkpoint file for the successful, neutral case, using SCF=3Dqc and = changing=20 the max number of steps to a higher number. 
 
I'm now able to get Gaussian to = converge the SCF=20 energy once.  Although how it does so is mysterious to me.  = This is=20 the output:
 
 It=3D668 PL=3D 1.00D-01 = DiagD=3DFF=20 ESCF=3D   1458.118125 Diff=3D 3.34D+01 RMSDP=3D = 6.02D-03.
 It=3D669=20 PL=3D 8.69D-02 DiagD=3DFF ESCF=3D   1269.316938 = Diff=3D-1.89D+01 RMSDP=3D=20 9.23D-03.
 It=3D670 PL=3D 1.04D-01 DiagD=3DFF = ESCF=3D   1062.608204=20 Diff=3D-2.07D+01 RMSDP=3D 8.57D-03.
 It=3D671 PL=3D 7.02D-02 = DiagD=3DFF=20 ESCF=3D   1325.914799 Diff=3D 2.63D+01 RMSDP=3D = 6.15D-03.
 It=3D672=20 PL=3D 8.38D-02 DiagD=3DFF ESCF=3D   1685.927152 Diff=3D = 3.60D+01 RMSDP=3D=20 1.08D-02.
 It=3D673 PL=3D 1.14D-01 DiagD=3DFF = ESCF=3D   1299.512442=20 Diff=3D-3.86D+01 RMSDP=3D 9.21D-03.
 It=3D674 PL=3D 9.54D-02 = DiagD=3DFF=20 ESCF=3D   1241.061125 Diff=3D-5.85D+00 RMSDP=3D = 5.78D-03.
 It=3D675=20 PL=3D 8.09D-02 DiagD=3DFF ESCF=3D   1278.716278 Diff=3D = 3.77D+00 RMSDP=3D=20 9.87D-03.
 It=3D676 PL=3D 9.82D-02 DiagD=3DFF = ESCF=3D   1361.857650=20 Diff=3D 8.31D+00 RMSDP=3D 9.23D-03.
 It=3D677 PL=3D 1.29D-01 = DiagD=3DFF=20 ESCF=3D   1536.868164 Diff=3D 1.75D+01 RMSDP=3D = 6.07D-03.
 It=3D678=20 PL=3D 6.85D-02 DiagD=3DFF ESCF=3D   1271.661599 = Diff=3D-2.65D+01 RMSDP=3D=20 9.45D-03.
 It=3D679 PL=3D 7.64D-02 DiagD=3DFF = ESCF=3D   =20 929.155505 Diff=3D-3.43D+01 RMSDP=3D 8.54D-03.
 It=3D680 PL=3D = 1.07D-01 DiagD=3DFF=20 ESCF=3D   1485.405483 Diff=3D 5.56D+01 RMSDP=3D = 6.20D-03.
 It=3D681=20 PL=3D 8.53D-02 DiagD=3DFF ESCF=3D   1551.560355 Diff=3D = 6.62D+00 RMSDP=3D=20 9.85D-03.
 It=3D682 PL=3D 8.91D-02 DiagD=3DFF = ESCF=3D   1008.530183=20 Diff=3D-5.43D+01 RMSDP=3D 8.72D-03.
 It=3D683 PL=3D 8.29D-02 = DiagD=3DFF=20 ESCF=3D   1254.460730 Diff=3D 2.46D+01 RMSDP=3D = 5.82D-03.
 It=3D684=20 PL=3D 9.05D-02 DiagD=3DFF ESCF=3D   1373.782809 Diff=3D = 1.19D+01 RMSDP=3D=20 9.83D-03.
 It=3D685 PL=3D 8.17D-02 DiagD=3DFF = ESCF=3D   1067.847535=20 Diff=3D-3.06D+01 RMSDP=3D 9.15D-03.
 It=3D686 PL=3D 7.68D-02 = DiagD=3DFF=20 ESCF=3D   1398.571380 Diff=3D 3.31D+01 RMSDP=3D = 6.08D-03.
 It=3D687=20 PL=3D 9.61D-02 DiagD=3DFF ESCF=3D   1666.016422 Diff=3D = 2.67D+01 RMSDP=3D=20 1.09D-02.
 It=3D688 PL=3D 9.80D-02 DiagD=3DFF = ESCF=3D   1357.094370=20 Diff=3D-3.09D+01 RMSDP=3D 9.29D-03.
It=3D689 PL=3D 5.77D-02 DiagD=3DFF = ESCF=3D  =20 1270.824001 Diff=3D-8.63D+00 RMSDP=3D 5.86D-03.
It=3D690 PL=3D = 6.98D-02 DiagD=3DFF=20 ESCF=3D   1391.204663 Diff=3D 1.20D+01 RMSDP=3D = 9.97D-03.
 

 ALL CONVERGERS ARE NOW FORCED = ON
 SHIFT=3D1000, PULAY ON, CAMP-KING ON
 AND ITERATION = COUNTER=20 RESET
 

 It=3D  1 PL=3D 3.95D-02 = DiagD=3DTT ESCF=3D=20 -41220.458895 Diff=3D-4.13D+03 RMSDP=3D 9.97D-03.
 It=3D  2 = PL=3D 3.95D-02=20 DiagD=3DTT ESCF=3D   1627.826035 Diff=3D 4.28D+03 RMSDP=3D=20 9.97D-03.
 It=3D  3 PL=3D 3.95D-02 DiagD=3DTT = ESCF=3D  =20 1554.928765 Diff=3D-7.29D+00 RMSDP=3D 9.97D-03.
 It=3D  4 = PL=3D 3.95D-02=20 DiagD=3DTT ESCF=3D   1457.010912 Diff=3D-9.79D+00 RMSDP=3D=20 9.97D-03.
 It=3D  4 PL=3D 3.95D-02 DiagD=3DTT = ESCF=3D  =20 1311.192626 Diff=3D-9.79D+00 RMSDP=3D 9.97D-03.
 It=3D  4 = PL=3D 3.95D-02=20 DiagD=3DTT ESCF=3D   1127.086921 Diff=3D-9.79D+00 RMSDP=3D=20 9.97D-03.
 It=3D  4 PL=3D 3.95D-02 DiagD=3DTT = ESCF=3D   =20 992.289552 Diff=3D-9.79D+00 RMSDP=3D 9.97D-03.
 It=3D  4 = PL=3D 3.95D-02=20 DiagD=3DTT ESCF=3D    821.787194 Diff=3D-9.79D+00 = RMSDP=3D=20 9.97D-03.
 It=3D  4 PL=3D 3.95D-02 DiagD=3DTT = ESCF=3D   =20 840.269011 Diff=3D-9.79D+00 RMSDP=3D 9.97D-03.
 It=3D  4 = PL=3D 3.95D-02=20 DiagD=3DTT ESCF=3D    800.888717 Diff=3D-9.79D+00 = RMSDP=3D=20 9.97D-03.
 It=3D  5 PL=3D 3.95D-02 DiagD=3DTT = ESCF=3D   =20 780.249572 Diff=3D-6.77D+01 RMSDP=3D 9.97D-03.
 It=3D  5 = PL=3D 3.95D-02=20 DiagD=3DTT ESCF=3D    730.748452 Diff=3D-6.77D+01 = RMSDP=3D=20 9.97D-03.
 It=3D  5 PL=3D 3.95D-02 DiagD=3DTT = ESCF=3D   =20 778.807603 Diff=3D-6.77D+01 RMSDP=3D 9.97D-03.
 It=3D  5 PL=3D 3.95D-02 = DiagD=3DTT=20 ESCF=3D    708.473922 Diff=3D-6.77D+01 RMSDP=3D=20 9.97D-03.
 It=3D  6 PL=3D 3.95D-02 DiagD=3DTT = ESCF=3D   =20 706.453896 Diff=3D-7.38D+00 RMSDP=3D 9.97D-03.
 It=3D  6 = PL=3D 3.95D-02=20 DiagD=3DTT ESCF=3D    700.609511 Diff=3D-7.38D+00 = RMSDP=3D=20 9.97D-03.
 It=3D  6 PL=3D 3.95D-02 DiagD=3DTT = ESCF=3D   =20 707.578870 Diff=3D-7.38D+00 RMSDP=3D 9.97D-03.
 It=3D  6 = PL=3D 3.84D-05=20 DiagD=3DTT ESCF=3D    700.075476 Diff=3D-7.38D+00 = RMSDP=3D=20 9.97D-03.
 It=3D  6 PL=3D 3.84D-05 DiagD=3DTT = ESCF=3D   =20 697.862649 Diff=3D-7.38D+00 RMSDP=3D 9.97D-03.
 It=3D  6 = PL=3D 3.84D-05=20 DiagD=3DTT ESCF=3D    696.972832 Diff=3D-7.38D+00 = RMSDP=3D=20 9.97D-03.
 It=3D  6 PL=3D 3.84D-05 DiagD=3DTT = ESCF=3D   =20 697.097586 Diff=3D-7.38D+00 RMSDP=3D 9.97D-03.
 It=3D  7 = PL=3D 3.84D-05=20 DiagD=3DTT ESCF=3D    696.168985 Diff=3D-1.03D+00 = RMSDP=3D=20 9.97D-03.
 
As you can see, the first 600+ = iterations, the ESCF=20 oscillates, but after the ALL CONVERGERS ARE NOW FORCED ON SHIFT=3D1000, = PULAY ON,=20 CAMP-KING ON AND ITERATION COUNTER RESET
 
it seems to settle down and = eventually=20 converges.  However, then it does a geometric optimization step, = and the=20 ESCF no longer converges.  It oscillates until I finally get the = UNABLE TO=20 ACHIEVE SELF-CONSISTENCE error...
 
First, what is this ALL CONVERGES = ARE NOW=20 FORCED ON SHIFT=3D1000....  step?
 
And secondly, why when Gaussian = has moved the=20 atoms a little bit to do the geometric optimization part, does the SCF=20 convergence become problematic again? 
 
I'm not progressing very far in = this=20 calculation and I am very perplexed at what to do = next.
 
Can someone tell me what I am = doing=20 wrong?
 
Thank you,
 
Connie


 
------=_NextPart_000_000B_01C28B66.37FC6C90-- From chemistry-request@server.ccl.net Thu Nov 14 00:06:11 2002 Received: from nmr-v.ioc.ac.ru ([193.233.3.213]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAE566D18386 for ; Thu, 14 Nov 2002 00:06:10 -0500 Received: from ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.9.3/8.9.3) with ESMTP id IAA00452 for ; Thu, 14 Nov 2002 08:06:32 GMT Sender: val@nmr-v.ioc.ac.ru Message-ID: <3DD35988.54F14DBE@ioc.ac.ru> Date: Thu, 14 Nov 2002 08:06:32 +0000 From: Valentin Ananikov Reply-To: val@ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.13 i686) X-Accept-Language: ru, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Is Computational Chemistry a real science ? References: <00e801c28b2e$83c0c3c0$be00000a@LAQUICOM02> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit >Thus, Computational Chemistry is not a real science? It is a "complex" science, therefore including real and imaginary parts. :)) best regards, Valentin. ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow, 119991 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Wed Nov 13 17:58:38 2002 Received: from usryws04.merck.com ([155.91.6.40]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gADMwcD13100 for ; Wed, 13 Nov 2002 17:58:38 -0500 Received: from 155.91.2.6 by usryws04.merck.com with ESMTP (SMTP Relay ( MMS v4.7);); Wed, 13 Nov 2002 17:58:37 -0500 X-Server-Uuid: 7a42c1b6-0774-11d5-89f7-00508bcf402e Received: from usrygw03.merck.com (usrygw03.merck.com [54.3.102.169]) by mmh1.merck.com (PMDF V6.0-24 #37353) with ESMTP id <01KOTTNVRSFU00525I@mmh1.merck.com> for CHEMISTRY@ccl.net; Wed, 13 Nov 2002 17:58:33 -0500 (EST) Received: by usrygw03.merck.com with Internet Mail Service (5.5.2656.59) id ; Wed, 13 Nov 2002 17:58:33 -0500 Content-return: allowed Date: Wed, 13 Nov 2002 17:58:28 -0500 From: "Gao, Ying-Duo" Subject: CHARMM force To: CHEMISTRY@ccl.net Message-ID: MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) X-WSS-ID: 11CC0697878357-01-01 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! Could anyone tell me, in CHARMM, how to print out force array on atoms? Thanks, Ying ------------------------------------------------------------------------------ Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (Whitehouse Station, New Jersey, USA) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it. ============================================================================== From chemistry-request@server.ccl.net Wed Nov 13 18:17:59 2002 Received: from mail.rpi.edu ([128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gADNHxD13353 for ; Wed, 13 Nov 2002 18:17:59 -0500 Received: from rpi.edu (omniocular-22.dynamic.rpi.edu [128.113.135.31]) by mail.rpi.edu (8.12.1/8.12.1) with ESMTP id gADNHlgp243718 for ; Wed, 13 Nov 2002 18:17:47 -0500 Message-ID: <3DD2DE3B.331E9EAC@rpi.edu> Date: Wed, 13 Nov 2002 18:20:28 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Is Computational Chemistry a real science ? References: <00e801c28b2e$83c0c3c0$be00000a@LAQUICOM02> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.3 (www dot roaringpenguin dot com slash mimedefang) Folks, I think it's time to take a step back, consider the origins of modern Computational Chemistry, and recognize that there are some very different subtypes of this activity. In my view, one flavor of Comp Chem grew from the need for theorists (read: Physical Chemists) to automate algorithms otherwise impractical to apply analytically (quantum chemistry, stat mech...etc come to mind here). Another type arose from the Physical Organic Chemistry community, where computational methods became another tool for probing reaction mechanisms, transition states, thermochemistry and related phenomena. Molecular mechanics represents a sort of a middle ground, where the development of potentials and minimizers is a P-Chem exercise, but some of these methods have nearly become a commodity item. A lot of Computational Chemistry is done to probe the scope and applicability of various implementations of force-field methods to address specific problems. We actually have a problem in semantics - who is the Computational Chemist? The one who develops the methods, or the one who is familiar with the field and applies the appropriate methods to solve specific problems? It would seem that a lot of product-oriented work is accomplished by the latter type of Computational Chemist, but not without the contributions of the former. Curt Breneman RPI Chemistry "Dr. Daniel Glossman-Mitnik" wrote: > > > On Tuesday, November 12, 2002, James Robinson wrote: > > ... So there is an added advantage. They have experience of > real science before attempting the computation > > Thus, Computational Chemistry is not a real science? Everyone in > this list agrees with this assert ? Best > regards Dr. Daniel > Glossman-Mitnik **************************************************************************** > > Dr. Daniel Glossman-Mitnik > Centro de Investigacion en Materiales Avanzados (CIMAV) > LAQUICOM - Laboratorio de Quimica Computacional > Miguel de Cervantes 120 - Complejo Industrial Chihuahua > Chihuahua, Chih. 31109 - Mexico > Phone: (52) 614 4391151 FAX: (52) 614 4391112 > E-mail: daniel.glossman@cimav.edu.mx > glossman@hotmail.com > dglossman@yahoo.com > > *************************************************************************** From chemistry-request@server.ccl.net Thu Nov 14 10:53:27 2002 Received: from techunix.technion.ac.il ([132.68.1.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAEFrQD01036 for ; Thu, 14 Nov 2002 10:53:26 -0500 Received: from tx.technion.ac.il (localhost [127.0.0.1]) by techunix.technion.ac.il (Postfix) with ESMTP id 3F4CC15642 for ; Thu, 14 Nov 2002 17:53:18 +0200 (IST) Sender: chrirena@techunix.technion.ac.il Message-ID: <3DD3C6ED.73383D2B@tx.technion.ac.il> Date: Thu, 14 Nov 2002 17:53:18 +0200 From: Irena Efremenko Organization: Technion - Israel Institute of Technology X-Mailer: Mozilla 4.78 [en] (X11; U; SunOS 5.8 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: RAID5 help needed Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Linux experts, My computer running RedHat 7.1 and software RAID 5 of 3 scsi disks fails to boot. It is very important for me to alive it since I have no backup. The only reasonable way is probably new system installation witout partitining. Using disc druid from manual graphic installation package, in Partitions section I see the following: Mount point Device Requested Actual Type sda1 15M 15 M Linux Native sda2 1027M 1027M Linux RAID sda3 305M 305M Linux swap sda5 3702M 3702M Linux RAID sda6 3624M 3624M Linux RAID The same for sdb and sdc, i.e. sdb1 15M 15 M Linux Native sdc1 15M 15 M Linux Native I suppose the original partition was standard for linux. Please, teach me how to edit this partitions to boot the system. Attached is the error file I've got trying to upgrade the system. Maybe it will help to understand my problem. Thanks in advance, _______________________________________________________________________________ Dr. Irena Efremenko e-mail: chrirena@tx.technion.ac.il Department of Chemical Engeneering, Technion, Israel Institute of Technology Haifa, 32000, Israel Tel. (972)-4-8293561 Fax. (972)-4-8230476 _______________________________________________________________________________ From chemistry-request@server.ccl.net Thu Nov 14 11:04:30 2002 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAEG4TD01280 for ; Thu, 14 Nov 2002 11:04:29 -0500 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr@ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id RAA28916 for ; Thu, 14 Nov 2002 17:04:28 +0100 Received: (qmail 16540 invoked by uid 525); 14 Nov 2002 16:04:28 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 14 Nov 2002 16:04:28 -0000 Date: Thu, 14 Nov 2002 17:04:28 +0100 (CET) From: To: Valentin Ananikov cc: chemistry@ccl.net Subject: Re: CCL:Is Computational Chemistry a real science ? In-Reply-To: <3DD35988.54F14DBE@ioc.ac.ru> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > >Thus, Computational Chemistry is not a real science? > > It is a "complex" science, therefore including real and > imaginary parts. :)) Im agree this definition. :)) Best, Csaba ------ Csaba Hetenyi, MSc, PhD Dept. of Medical Chemistry, University of Szeged, 8 Dom ter, Szeged 6720, Hungary From chemistry-request@server.ccl.net Thu Nov 14 12:34:09 2002 Received: from web80310.mail.yahoo.com ([66.218.79.26]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gAEHY9D03242 for ; Thu, 14 Nov 2002 12:34:09 -0500 Message-ID: <20021114173408.52220.qmail@web80310.mail.yahoo.com> Received: from [207.225.232.131] by web80310.mail.yahoo.com via HTTP; Thu, 14 Nov 2002 09:34:08 PST Date: Thu, 14 Nov 2002 09:34:08 -0800 (PST) From: Gustavo Mercier Reply-To: gamercier@yahoo.com Subject: Re: CCL:Is Computational Chemistry a real science ? To: chemistry@ccl.net In-Reply-To: <3DD2DE3B.331E9EAC@rpi.edu> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1003430935-1037295248=:52094" --0-1003430935-1037295248=:52094 Content-Type: text/plain; charset=us-ascii Hi! As "former" comp. chemist who did most of his work when the term was not fashionable, I'll throw my 0.02 of opinion. I think Curt is on the right track... Computational Chemistry may have had its origin in the theoretical work from Physical Chemistry, but today this field is very broad and embraces many areas. Curt writes about Physical Organic Chemistry. I would add other fields such as Biology/Biochemistry, Pharmacology, Statistics, Numerical Analysis, and Computer Science. For example, consider data mining applications that emphasize algorithms developed in Computer Science with a scoring function (that may or may not have a foundation on Physical Chemistry or Physical Organic Chemistry) to search for new lead compounds in drug development. Those individuals that code and make developments in theoretical physical chemistry with a more "classical" view of chemistry in their minds may feel that their work is very different from the example I described. Some may even feel that it is not CC! I would disagree and I think that the breath of topics covered by the many journals in CC are consistent with my view. It is unfortunate that some feel that CC is not a "real" science. It is sad to see this "prejudice" perpetuated over 20 years! The contributions of CC are real. CC has grown and Pople's Noble prize is a reaffirmation of the significance of CC. I probably do not have to remind members of this list that Pople and his group have worked in both theoretical physical chemistry and computer science (not to mention numerical methods, etc.) to bring Gaussian to life. The publication of the Reviews of Computational Chemistry and the longevity and popularity of this list are other landmarks that speak of the significance and reality of CC as a science. More important it shows that the field is mature. Slowly the field gets defined. The journals, meetings, Reviews, and this list help to do that. It is now creeping into the chemistry curriculum. With time I have no doubt that it will be another specialty in Chemistry. Depending on the strengths of the departments it may have different flavors - more theory oriented or more physical chemistry or more computer science, etc. Finally, let me end with a comment on the issue of "computer work" as science. There is a line of thinking that takes computer simulations as just another "experimental tool". The experiment is not in a beaker, but in a machine - not different from a NMR machine. The exception is that an artificial (virtual) world that is normally very simple is created within the computer. It is this "world" that is being observed and measured. This is the kind of thinking that S. Wolfram discusses in his book a "New Kind of Science". (I know that his approach may be a bit pompous and has generated significant criticism, but there is still a valid point to his argument.) Experimentation (eg. simulation) within the virtual world created within a computer is an extension of our traditional experimental science. The success of the traditional science together with computer and other technologies allow us to evolve the concept of science without taking away from the foundation we have from experimenting with the natural world. Enjoy! Bye! Gustavo Mercier, Jr. "Curt M. Breneman" <brenec@rpi.edu> wrote: Folks, I think it's time to take a step back, consider the origins of modern Computational Chemistry, and recognize that there are some very different subtypes of this activity. In my view, one flavor of Comp Chem grew from the need for theorists (read: Physical Chemists) to automate algorithms otherwise impractical to apply analytically (quantum chemistry, stat mech...etc come to mind here). Another type arose from the Physical Organic Chemistry community, where computational methods became another tool for probing reaction mechanisms, transition states, thermochemistry and related phenomena. Molecular mechanics represents a sort of a middle ground, where the development of potentials and minimizers is a P-Chem exercise, but some of these methods have nearly become a commodity item. A lot of Computational Chemistry is done to probe the scope and applicability of various implementations of force-field methods to address specific problems. We actually have a problem in semantics - who is the Computational Chemist? The one who develops the methods, or the one who is familiar with the field and applies the appropriate methods to solve specific problems? It would seem that a lot of product-oriented work is accomplished by the latter type of Computational Chemist, but not without the contributions of the former. Curt Breneman RPI Chemistry -- Gustavo A. Mercier, Jr., MD,PhD Seattle Nuclear Medicine & U/S Associates 1229 Madison, Suite 1150 Seattle, WA 98104-1377 voice: 206-386-6300; fax: 206-386-6312 gamercier@yahoo.com --------------------------------- Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! --0-1003430935-1037295248=:52094 Content-Type: text/html; charset=us-ascii

Hi!

As "former" comp. chemist who did most of his work when the term was not fashionable, I'll throw my 0.02 of opinion.

I think Curt is on the right track...

Computational Chemistry may have had its origin in the theoretical work from Physical Chemistry, but today this field is very broad and embraces many areas. Curt writes about Physical Organic Chemistry. I would add other fields such as Biology/Biochemistry, Pharmacology, Statistics, Numerical Analysis, and Computer Science. For example, consider data mining applications that emphasize algorithms developed in Computer Science with a scoring function (that may or may not have a foundation on Physical Chemistry or Physical Organic Chemistry) to search for new lead compounds in drug development. Those individuals that code and make developments in theoretical physical chemistry with a more "classical" view of chemistry in their minds may feel that their work is very different from the example I described. Some may even feel that it is not CC! I would disagree and I think that the breath of topics covered by the many journals in CC are consistent with my view.

It is unfortunate that some feel that CC is not a "real" science. It is sad to see this "prejudice" perpetuated over 20 years! The contributions of CC are real. CC has grown and Pople's Noble prize is a reaffirmation of the significance of CC. I probably do not have to remind members of this list that Pople and his group have worked in both theoretical physical chemistry and computer science (not to mention numerical methods, etc.) to bring Gaussian to life.

The publication of the Reviews of Computational Chemistry and the longevity and popularity of this list are other landmarks that speak of the significance and reality of CC as a science. More important it shows that the field is mature. Slowly the field gets defined. The journals, meetings, Reviews, and this list help to do that. It is now creeping into the chemistry curriculum. With time I have no doubt that it will be another specialty in Chemistry. Depending on the strengths of the departments it may have different flavors - more theory oriented or more physical chemistry or more computer science, etc.

Finally, let me end with a comment on the issue of "computer work" as science. There is a line of thinking that takes computer simulations as just another "experimental tool". The experiment is not in a beaker, but in a machine - not different from a NMR machine. The exception is that an artificial (virtual) world that is normally very simple is created within the computer. It is this "world" that is being observed and measured. This is the kind of thinking that S. Wolfram discusses in his book a "New Kind of Science". (I know that his approach may be a bit pompous and has generated significant criticism, but there is still a valid point to his argument.) Experimentation (eg. simulation) within the virtual world created within a computer is an extension of our traditional experimental science. The success of the traditional science together with computer and other technologies allow us to evolve the concept of science without taking away from the foundation we have from experimenting with the natural world.

Enjoy!

Bye!

Gustavo Mercier, Jr.

 

  "Curt M. Breneman" &lt;brenec@rpi.edu&gt; wrote:

Folks,

I think it's time to take a step back, consider the origins of modern
Computational Chemistry, and recognize that there are some very
different subtypes of this activity. In my view, one flavor of Comp
Chem grew from the need for theorists (read: Physical Chemists) to
automate algorithms otherwise impractical to apply analytically (quantum
chemistry, stat mech...etc come to mind here). Another type arose from
the Physical Organic Chemistry community, where computational methods
became another tool for probing reaction mechanisms, transition states,
thermochemistry and related phenomena. Molecular mechanics represents a
sort of a middle ground, where the development of potentials and
minimizers is a P-Chem exercise, but some of these methods have nearly
become a commodity item. A lot of Computational Chemistry is done to
probe the scope and applicability of various implementations of
force-field methods to address specific problems.

We actually have a problem in semantics - who is the Computational
Chemist? The one who develops the methods, or the one who is familiar
with the field and applies the appropriate methods to solve specific
problems? It would seem that a lot of product-oriented work is
accomplished by the latter type of Computational Chemist, but not
without the contributions of the former.

Curt Breneman
RPI Chemistry




--
Gustavo A. Mercier, Jr., MD,PhD
Seattle Nuclear Medicine & U/S Associates
1229 Madison, Suite 1150
Seattle, WA 98104-1377
voice: 206-386-6300; fax: 206-386-6312
gamercier@yahoo.com 


Do you Yahoo!?
New DSL Internet Access from SBC & Yahoo! --0-1003430935-1037295248=:52094-- From chemistry-request@server.ccl.net Thu Nov 14 09:02:29 2002 Received: from smtp.laposte.net ([213.30.181.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAEE2SD31210 for ; Thu, 14 Nov 2002 09:02:29 -0500 Received: from nouveaupc (80.13.205.188) by smtp.laposte.net (6.0.053) id 3DB5C8A000243C4D for chemistry@ccl.net; Thu, 14 Nov 2002 15:02:23 +0100 Message-ID: <001101c28be6$714dfab0$3b96fea9@nouveaupc> From: "Alexandre Hocquet" To: References: <00e801c28b2e$83c0c3c0$be00000a@LAQUICOM02> <3DD2DE3B.331E9EAC@rpi.edu> Subject: Who is the Computational Chemist ? Date: Thu, 14 Nov 2002 15:02:16 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 > We actually have a problem in semantics - who is the Computational > Chemist? The one who develops the methods, or the one who is familiar > with the field and applies the appropriate methods to solve specific > problems? It would seem that a lot of product-oriented work is > accomplished by the latter type of Computational Chemist, but not > without the contributions of the former. But if you name "computational chemist" the one who develops the method, then who is the "theoretical chemist", in your view ? ------------------------------------------------------------ Alexandre HOCQUET Laboratoire de Physicochimie Biomoléculaire et Cellulaire UMR CNRS 7033 hocquet@ccr.jussieu.fr Fax: 33 1 44277560 LPBC, case courrier 138 4 Place Jussieu, 75252 PARIS Cedex 05 France ------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Nov 14 14:40:54 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAEJerD06477 for ; Thu, 14 Nov 2002 14:40:54 -0500 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id OAA11533 for ; Thu, 14 Nov 2002 14:40:53 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3DD3FC45.F5D8D9F8@cornell.edu> Date: Thu, 14 Nov 2002 14:40:53 -0500 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.16smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Question about Guassian98W -- stopping and restarting jobs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all -- I was wondering if any of you know how to stop a job and restart it at the exact point where you stopped it in Gaussian98W. The reason why I'm asking is that I'm using a computer cluster at school where there's a 24 hour time limit for jobs. My jobs typically last longer than that (2-4 days). I don't think the Guess=Read option is applicable here, but I could be wrong. Does anyone have experience with this? Thanks! Connie From chemistry-request@server.ccl.net Thu Nov 14 13:54:04 2002 Received: from web20604.mail.yahoo.com ([216.136.226.162]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gAEIs3D05312 for ; Thu, 14 Nov 2002 13:54:04 -0500 Message-ID: <20021114185403.75267.qmail@web20604.mail.yahoo.com> Received: from [206.111.112.115] by web20604.mail.yahoo.com via HTTP; Thu, 14 Nov 2002 10:54:03 PST Date: Thu, 14 Nov 2002 10:54:03 -0800 (PST) From: Sengen Sun Subject: Where should computational chemistry be? To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii “Computational chemistry” has a duality - independent science and non-independent science depending on how you look at it :-) For the grant or scholarship applications, where should the phrase “computational chemistry” be? My answer is nowhere. Nether under chemistry, nor under physical chemistry. A computational chemist could be a network or database administrator, and could be a computer programmer. Computational chemistry is too broad, and should be attached to specific scientific disciplines. It is better than to attach the scientific disciplines under computational chemistry. __________________________________________________ Do you Yahoo!? Yahoo! Web Hosting - Let the expert host your site http://webhosting.yahoo.com From chemistry-request@server.ccl.net Thu Nov 14 15:12:57 2002 Received: from front3.chartermi.net ([24.213.60.109]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAEKCvD07115 for ; Thu, 14 Nov 2002 15:12:57 -0500 Received: from [24.247.80.10] (HELO ws610) by front3.chartermi.net (CommuniGate Pro SMTP 3.5.9a) with SMTP id 28995669 for chemistry@ccl.net; Thu, 14 Nov 2002 15:12:57 -0500 Message-ID: <001401c28c1a$381ae440$0401a8c0@kressworks.com> Reply-To: From: To: "CCL" References: <00e801c28b2e$83c0c3c0$be00000a@LAQUICOM02> <3DD2DE3B.331E9EAC@rpi.edu> <001101c28be6$714dfab0$3b96fea9@nouveaupc> Subject: Re: CCL:Who is the Computational Chemist ? Date: Thu, 14 Nov 2002 15:12:54 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit 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 A theoretical chemist is a type of chemist whose existence is proposed but not experimentally verified. Jim ----- Original Message ----- From: "Alexandre Hocquet" To: Sent: Thursday, November 14, 2002 9:02 AM Subject: CCL:Who is the Computational Chemist ? > > > We actually have a problem in semantics - who is the Computational > > Chemist? The one who develops the methods, or the one who is familiar > > with the field and applies the appropriate methods to solve specific > > problems? It would seem that a lot of product-oriented work is > > accomplished by the latter type of Computational Chemist, but not > > without the contributions of the former. > > But if you name "computational chemist" the one who develops the method, > then who is the "theoretical chemist", in your view ? > > ------------------------------------------------------------ > Alexandre HOCQUET > Laboratoire de Physicochimie Biomoléculaire et Cellulaire > UMR CNRS 7033 > hocquet@ccr.jussieu.fr > Fax: 33 1 44277560 > LPBC, case courrier 138 > 4 Place Jussieu, 75252 PARIS Cedex 05 France > ------------------------------------------------------------ > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Nov 14 15:10:07 2002 Received: from phobos.email.Arizona.EDU ([128.196.133.165]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAEKA7D07061 for ; Thu, 14 Nov 2002 15:10:07 -0500 Received: from u.arizona.edu (128.196.184.158) by phobos.email.Arizona.EDU (6.0.053) (authenticated as mcafiero@email.arizona.edu) id 3DD39B0000014C65; Thu, 14 Nov 2002 13:10:06 -0700 Sender: mcafiero@ccl.net Message-ID: <3DD4031A.E1915CFF@u.arizona.edu> Date: Thu, 14 Nov 2002 20:10:02 +0000 From: Maurice Cafiero X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.13-7mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: Alexandre Hocquet CC: chemistry@ccl.net Subject: Re: CCL:Who is the Computational Chemist ? References: <00e801c28b2e$83c0c3c0$be00000a@LAQUICOM02> <3DD2DE3B.331E9EAC@rpi.edu> <001101c28be6$714dfab0$3b96fea9@nouveaupc> Content-Type: multipart/alternative; boundary="------------53FCCB0839710B04F8205804" --------------53FCCB0839710B04F8205804 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hello: It is accepted in several places I have seen that the theoretical chemist is the "method developer" or the "programmer," while the computational chemist is the "user" who is comfortable with not only black boxes like Gaussian but also the less black box like Gamess and Dalton (and knows what all the output means!). The "experimentalist cum computational chemist" is the strictly Gaussian type user. It is ridiculous to say that computational chemistry (CC) is a separate science. The problem is that from the chemistry point of view it seems very alien. Even, in many cases, to the experimental physical chemist. From the Physics point of view it is plainly obvious that CC or TC (theoretical) are small subsets of QM or even CM. Perhaps rather than teach CC or TC in chemistry departments it be taught in physics departments or in inter-disciplinary departments like the quantum theory project. -- Mauricio Cafiero Doctoral Candidate : Theoretical and Computational Quantum Chemistry Department of Chemistry University of Arizona --------------53FCCB0839710B04F8205804 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit hello:
    It is accepted in several places I have seen that the theoretical chemist is the "method developer"
or the "programmer," while the computational chemist is the "user" who is comfortable with not only black boxes like
Gaussian but also the less black box like Gamess and Dalton (and knows what all the output means!). The "experimentalist cum computational chemist" is the strictly Gaussian type user.
    It is ridiculous to say that computational chemistry (CC) is a separate science. The problem is that from the chemistry point of view it seems very alien. Even, in many cases, to the experimental physical chemist.  From the Physics point of view it is plainly obvious that CC or TC (theoretical) are small subsets of QM or even CM. Perhaps rather than teach CC or TC in chemistry departments it be taught in physics departments or in inter-disciplinary departments like the quantum theory project. 
-- 
Mauricio Cafiero
Doctoral Candidate : Theoretical
                     and Computational
                     Quantum Chemistry
Department of Chemistry
University of Arizona
  --------------53FCCB0839710B04F8205804-- From chemistry-request@server.ccl.net Thu Nov 14 14:39:51 2002 Received: from fw-mail2.novartis.com ([194.191.169.76]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAEJdoD06452; Thu, 14 Nov 2002 14:39:50 -0500 Received: from mtap1.is.chbs (mtap1.novartis.com [192.37.33.20]) by fw-mail2.novartis.com (8.11.6/8.11.6) with ESMTP id gAEJcrO131164; Thu, 14 Nov 2002 20:38:53 +0100 Received: from phchbs-s3025.EU.novartis.net (phchbs-s3025.eu.novartis.net [192.37.31.249]) by mtap1.is.chbs (8.11.3/8.11.3) with ESMTP id gAEJdon86996; Thu, 14 Nov 2002 20:39:50 +0100 To: "Alexandre Hocquet" Cc: chemistry@ccl.net, "Computational Chemistry List" Subject: Re: CCL:Who is the Computational Chemist ? MIME-Version: 1.0 Message-ID: From: anthony.klon@pharma.novartis.com Date: Thu, 14 Nov 2002 14:40:46 -0500 Content-Type: multipart/alternative; boundary="=_alternative 006C1A2285256C71_=" This is a multipart message in MIME format. --=_alternative 006C1A2285256C71_= Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, As my postdoctoral advisor said, 'the computational chemists are the ones who actually do the typing, the theoretical chemists are those who just think about doing the typing.' On a more serious note, my thesis advisor in graduate school (who was a=20 theoretician) encouraged all of his students to have an experimental=20 component to their thesis, which was carried out in laboratory of a=20 collaborator. As a result (using the teminology introduced so far), we=20 had a mixture of theoretical chemists (those who developed code),=20 computational chemists (those who used code), as well as x-ray=20 crystallographers, fluorescence spectroscopists, as well as people=20 dabbling in molecular biology and cryo-EM. It was an excellent example of = the interplay between theoretical and experimental methods, with much of=20 the experimental methods providing information for computational projects=20 in structural biology, and theoretical methods being developed both to aid = the computational people in our group, who in turn provided predictive=20 models to their collaborators. The students that graduate from my old lab = tend to be distributed well throughout experimental and theoretical groups = in industry and academia, and I think we're all the stronger for our=20 mentor's philosophy. There's no such thing as a 'pure experimental' or 'pure theoretical'=20 science. Even experimentalists produce models (whether they realize it or = not!) at every stage of their work. And theoreticians have to test their=20 models out, whether it's on a computer or providing a prediction for the=20 experimentalists to take a whack at. I think it's difficult to define a=20 set of skills that would make a good computational chemist, as our lab was = in a Biochemistry Department and had individuals ranging from hard core=20 programmers, to those with mostly a biological background who were=20 basically end users. Anthony Klon "Alexandre Hocquet" Sent by: "Computational Chemistry List" 11/14/2002 09:02 AM =20 To: cc:=20 Subject: CCL:Who is the Computational Chemist ? > We actually have a problem in semantics - who is the Computational > Chemist? The one who develops the methods, or the one who is familiar > with the field and applies the appropriate methods to solve specific > problems? It would seem that a lot of product-oriented work is > accomplished by the latter type of Computational Chemist, but not > without the contributions of the former. But if you name "computational chemist" the one who develops the method, then who is the "theoretical chemist", in your view ? ------------------------------------------------------------ Alexandre HOCQUET Laboratoire de Physicochimie Biomol=E9culaire et Cellulaire UMR CNRS 7033 hocquet@ccr.jussieu.fr Fax: 33 1 44277560 LPBC, case courrier 138 4 Place Jussieu, 75252 PARIS Cedex 05 France ------------------------------------------------------------ -=3D This is automatically added to each message by mailing script =3D- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To=20 Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net --=_alternative 006C1A2285256C71_= Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,

As my postdoctoral advisor said,

'the computational chemists are the = ones who actually do the typing,
the theoretical chemists are those w= ho just think about doing the typing.'

On a more serious note, my thesis ad= visor in graduate school (who was a theoretician) encouraged all of his stu= dents to have an experimental component to their thesis, which was carried = out in laboratory of a collaborator.  As a result (using the teminolog= y introduced so far), we had a mixture of theoretical chemists (those who d= eveloped code), computational chemists (those who used code), as well as x-= ray crystallographers, fluorescence spectroscopists, as well as people dabb= ling in molecular biology and cryo-EM.  It was an excellent example of= the interplay between theoretical and experimental methods, with much of t= he experimental methods providing information for computational projects in= structural biology, and theoretical methods being developed both to aid th= e computational people in our group, who in turn provided predictive models= to their collaborators.  The students that graduate from my old lab t= end to be distributed well throughout experimental and theoretical groups i= n industry and academia, and I think we're all the stronger for our mentor'= s philosophy.

There's no such thing as a 'pure exp= erimental' or 'pure theoretical' science.  Even experimentalists produ= ce models (whether they realize it or not!) at every stage of their work. &= nbsp;And theoreticians have to test their models out, whether it's on a com= puter or providing a prediction for the experimentalists to take a whack at= .  I think it's difficult to define a set of skills that would make a = good computational chemist, as our lab was in a Biochemistry Department and= had individuals ranging from hard core programmers, to those with mostly a= biological background who were basically end users.

Anthony Klon





"Alexandre Hocquet" <= ;alexandre.hocquet@laposte.net>
Sent by: "Computational Chemist= ry List" <chemistry-request@ccl.net>

11/14/2002 09:02 AM

       
        To: &nbs= p;      <chemistry@ccl.net>
        cc: &nbs= p;      
        Subject:=        CCL:Who is the Computational Chemist ?



> We actually have a problem in semantics - who is the Computational
> Chemist?  The one who develops the methods, or the one who is fam= iliar
> with the field and applies the appropriate methods to solve specific > problems?  It would seem that a lot of product-oriented work is > accomplished by the latter type of Computational Chemist, but not
> without the contributions of the former.

But if you name "computational chemist" the one who develops the = method,
then who is the "theoretical chemist", in your view ?

------------------------------------------------------------
Alexandre HOCQUET
Laboratoire de Physicochimie Biomol=E9culaire et Cellulaire
UMR CNRS 7033
hocquet@ccr.jussieu.fr
Fax: 33 1 44277560
LPBC, case courrier 138
4 Place Jussieu, 75252 PARIS Cedex 05 France
------------------------------------------------------------





-=3D This is automatically added to each message by mailing script =3D-
CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To A= dmins
Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | = Jan: jkl@ccl.net

--=_alternative 006C1A2285256C71_=-- From chemistry-request@server.ccl.net Thu Nov 14 16:04:22 2002 Received: from exchange.neokimia.com ([132.210.158.207]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAEL4MD08251 for ; Thu, 14 Nov 2002 16:04:22 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 content-class: urn:content-classes:message Subject: RE: software for ligand-receptor interaction energy evaluation ? MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 14 Nov 2002 16:03:01 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: software for ligand-receptor interaction energy evaluation ? Thread-Index: AcKKeX/CrTwau0v4R5SF1H/oUdUJegBpIuxg From: "Axel Mathieu" To: "Nikolaus Stiefl" , "CCL" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gAEL4MD08252 You know, there are several types of programs and scoring functions that can do these types of calculations but there is one is particular that I'd like mention. All these programs have their strong points and weaknesses and it will be your task to determine if the program suits your resaerch (protein) appropriately. The program in question is called STC (for structure-based thermodynamics calculations) developped by U of Alberta and should still be free. This program is a UNIX based program that can calculate binding energies using sovent accessible surface area (ASA), and has been shown to be quite precise in certain cases (nothing is good for ALL applications in comp chem!). Nonetheless, I used STC to perform thermodynamic calculations to propose a mechanism for my protein of interest during my Ph.D. Take a look, you can find all the info at: http://www.pence.ualberta.ca/ftp/stc/index.html Structure based thermodynamic calculations are not new and have actually been around for a quite a long time now. These calculations should give you interesting results. The program is very easy to use (so long as you understand a bit of the theory) and its turns out theoretical binding constants very fast. Now I don't know your background, but if thermodynamics isn't your thing, I don't suggest using it. Otherwise, you should be able to pull out some nice hypotheses and theoretical results. I want to be clear though, this is not an automated docking program; you need the coordinates of the ligand and receptor (in pdb files) and you have to test different binding "modes" seperately. Moreover, it is particularly useful (and easy to use) if your ligand binds to a solvent accessible site since the calculations are based on ASA. This program is good when you know how the ligand binds to the receptor and/or are proposing a mechanims of ligand binding. If that is not the case for you, get back to me and I'll explain you how I used it for a non solvent accessible binding site ... Good Luck! Axel -----Original Message----- From: Nikolaus Stiefl [mailto:nikolaus.stiefl@mail.uni-wuerzburg.de] Sent: 12 novembre, 2002 12:15 To: chemistry@ccl.net Subject: CCL:software for ligand-receptor interaction energy evaluation ? Hi, a colleague of mine asked me if I could calculate interaction energies between a ligand and a receptor into which he docked some compounds. I had a look at some of the complexes and it seems like he wants to use this for a reevaluation of the activity of his docked structures. Unfortunately I am not too much into this sort of energy calculations and now I am looking for a freeware program that is able to do that with not too much effort. I would be very grateful if anybody could point me into a direction. Cheers Nik -- Nikolaus Stiefl Chemometriks and Drug Design University Wuerzburg Dept. of Pharmacy Am Hubland D-97074 Wuerzburg Germany Phone: +49 - 931 8885473 -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Nov 14 15:38:28 2002 Received: from pollux.chem.umn.edu ([128.101.156.56]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAEKcSD07802 for ; Thu, 14 Nov 2002 15:38:28 -0500 Received: (from cramer@localhost) by pollux.chem.umn.edu (8.9.3/8.9.3) id OAA22324 for chemistry@ccl.net; Thu, 14 Nov 2002 14:38:28 -0600 (CST) From: Christopher Cramer Message-Id: <200211142038.OAA22324@pollux.chem.umn.edu> Subject: Definitions of terms To: chemistry@ccl.net Date: Thu, 14 Nov 2002 14:38:27 -0600 (CST) X-Mailer: ELM [version 2.5 PL2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Re below thread. > > > We actually have a problem in semantics - who is the Computational > > Chemist? The one who develops the methods, or the one who is familiar > > with the field and applies the appropriate methods to solve specific > > problems? It would seem that a lot of product-oriented work is > > accomplished by the latter type of Computational Chemist, but not > > without the contributions of the former. > > But if you name "computational chemist" the one who develops the method, > then who is the "theoretical chemist", in your view ? > I have done my best to stay out of this conversation over the last few days because I do not want to appear as though I am indulging in a shameless marketing ploy. So many posts have, however, worn down my resolve, and I respond to the above question with a quote from Cramer, C. J. "Essentials of Computational Chemistry" Wiley, Chichester: 2002. "With all these definitions in hand, we may return to a point raised in the preface, namely, what is the difference between 'Theory', 'Molecular Modeling', and 'Computational Chemistry'? To the extent members of the community make distinctions, 'theorists' tend to have as their greatest goal the development of new theories and/or models that have improved performance or generality over existing ones. Researchers involved in 'molecular modeling' tend to focus on target systems having particular chemical relevance (e.g., for economic reasons) and to be willing to sacrifice a certain amount of theoretical rigor in favor of getting the right answer in an efficient manner. Finally, 'computational chemists' may devote themselves not to chemical aspects of the problem, per se, but to computer related aspects, e.g., writing improved algorithms for solving particularly difficult equations, or developing new ways to encode or visualize data, either as input to or output from a model. As with any classification scheme, there are no distinct boundaries recognized either by observers or by individual researchers, and certainly a given research undertaking may involve significant efforts undertaken within all three of the areas noted above. In the spirit of inclusiveness, we will treat the terms as essentially interchangeable." This is from the end of Section 1 of the first chapter entitled "What are Theory, Computation, and Modeling?" Wiley has made this chapter available in .pdf form on its website, on amazon.com, and I have a copy on my own website (http://pollux.chem.umn.edu/~cramer/Chapter_1.pdf) for any who feel sufficiently interested to peruse it. Chris -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (612) 597-5275 cramer@pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about new textbook "Essentials of Computational Chemistry: Theories and Models")