From chemistry-request@ccl.net Wed Jul 2 12:57:02 2003 Received: from leviathan.ele.uri.edu (leviathan.ele.uri.edu [131.128.51.64]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h62Gv1qe005412 for ; Wed, 2 Jul 2003 12:57:02 -0400 Received: from ele.uri.edu (ip68-9-19-36.ri.ri.cox.net [68.9.19.36]) by leviathan.ele.uri.edu (8.12.6/8.12.6) with ESMTP id h62Guv2S020520; Wed, 2 Jul 2003 12:56:58 -0400 (EDT) Message-ID: <3F030E4D.4000908(at)ele.uri.edu> Date: Wed, 02 Jul 2003 12:54:37 -0400 From: Su Wu User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Pradipta Bandyopadhyay , chemistry Subject: Re: CCL:interpolation code for 3d data !! References: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi Pradipta, I have done spline interpolation on x or y of A = f(x,y) in Matlab. If interested, the following is some help information on spline, or go to www.mathworks.com and search for 'spline'. Good luck! Su Wu SPLINE Cubic spline data interpolation. YY = SPLINE(X,Y,XX) uses cubic spline interpolation to find YY, the values of the underlying function Y at the points in the vector XX. The vector X specifies the points at which the data Y is given. If Y is a matrix, then the data is taken to be vector-valued and interpolation is performed for each column of Y and YY will be length(XX)-by-size(Y,2). PP = SPLINE(X,Y) returns the piecewise polynomial form of the cubic spline interpolant for later use with PPVAL and the spline utility UNMKPP. Ordinarily, the not-a-knot end conditions are used. However, if Y contains two more values than X has entries, then the first and last value in Y are used as the endslopes for the cubic spline. Namely: f(X) = Y(:,2:end-1), df(min(X)) = Y(:,1), df(max(X)) = Y(:,end) Example: This generates a sine curve, then samples the spline over a finer mesh: x = 0:10; y = sin(x); xx = 0:.25:10; yy = spline(x,y,xx); plot(x,y,'o',xx,yy) Example: This illustrates the use of clamped or complete spline interpolation where end slopes are prescribed. Zero slopes at the ends of an interpolant to the values of a certain distribution are enforced: x = -4:4; y = [0 .15 1.12 2.36 2.36 1.46 .49 .06 0]; cs = spline(x,[0 y 0]); xx = linspace(-4,4,101); plot(x,y,'o',xx,ppval(cs,xx),'-'); See also INTERP1, PPVAL, SPLINES (The Spline Toolbox). Pradipta Bandyopadhyay wrote: > Hi, > > I am looking for a code(in fortran) for interpolation of a large set > of 3 dimensional data (on an eqaully spaced grid). I tried the polynomial > routine in numerical recipe -but it is very poor for my data. Probably > spline or hermite polynomial based interpolation scheme would be the best. > I would appreciate any help. > > thanks. > > Pradipta > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY(at)ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST(at)ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl(at)ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Wed Jul 2 16:38:23 2003 Received: from mail.uh.edu (SanJacinto.Mail.UH.EDU [129.7.69.101]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h62KcNqe010506 for ; Wed, 2 Jul 2003 16:38:23 -0400 Received: from conversion-daemon by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0HHE00M01ZZU2I^at^mail.uh.edu> for chemistry^at^ccl.net; Wed, 2 Jul 2003 15:38:19 -0500 (CDT) Received: from localhost (Colorado.Mail.UH.EDU [129.7.69.103]) by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0HHE00KF3ZZTQP^at^mail.uh.edu> for chemistry^at^ccl.net; Wed, 02 Jul 2003 15:38:17 -0500 (CDT) Date: Wed, 02 Jul 2003 15:38:17 -0500 (CDT) From: Niharendu.Choudhury^at^mail.uh.edu Subject: Ewald in CHARMM To: chemistry^at^ccl.net Message-id: <482058488.1057178297881.JavaMail.root@localhost> MIME-version: 1.0 X-Mailer: Sun(TM) Web Access 1.2 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7BIT Hi all, Thanks to all who answered me earlier. I am in a new trouble. I was initially running with following crystal keywords: Crystal Define Cubic 24.850 24.850 24.850 90.0 90.0 90.0 Crystal Build noperations 0 and energy keywords : ENERGY ATOM ELEC EWALD KAPPA 0.21 KMAX 4 KSQMAX 27 - CUTNB 10.0 CUTIM 10.0 CTOFNB 9.5 VDW SHIFT it was running fine. Now I have changed the energy section to the following: ENERGY ATOM ELEC EWALD KAPPA 0.21 KMAX 4 KSQMAX 27 - CUTNB 12.0 CUTIM 12.0 CTOFNB 10 VDW SHIFT and it is not running. (I have only changed cutnb and ctofnb, crystal section same). Can anybody tell me why? Bye Niharendu Choudhury From chemistry-request@ccl.net Tue Jul 1 23:02:14 2003 Received: from smtp4.dti.ne.jp (smtp4.dti.ne.jp [202.216.228.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6232Cqe019039 for ; Tue, 1 Jul 2003 23:02:13 -0400 Received: from oemcomputer (PPP142.fukuoka-ip.dti.ne.jp [211.132.92.142]) by smtp4.dti.ne.jp (3.08s) with SMTP id h6231vAi005729 for ; Wed, 2 Jul 2003 12:02:00 +0900 (JST) Message-ID: <001c01c34045$b048fbc0$8e5c84d3@oemcomputer> From: "Telkuni" To: Subject: Re: How to get the orbital symmetry? -2 Date: Wed, 2 Jul 2003 11:57:34 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Jens, thanks for your kind reply. To summarize your comment, I must start with proper structure for Gaussian symmetry recognition. Now, I've just received a CCL message from Gaussian.Inc. (also you've received) It said that you should use "symm=loose" to the input. So, I'll calculate with yours and Gaussian's method. Sincerely yours, ---------------------------------------------------- Telkuni Tsuru telkuni)at(venus.dti.ne.jp ----- Original Message ----- From: "Jens Spanget-Larsen" To: "Telkuni" Sent: Monday, June 30, 2003 11:00 PM Subject: Re: CCL:How to get the orbital symmetry using Gaussian TDDFT ? > Telkuni: > > > With your words, must I continue the optimization until > > I have gotten the perfect nuclear coordinate? > > If it is so, I'll modify the optimization step(s). > > Dear Telkuni: > > If you want Gaussian to recognize the symmetry elements of a > particular point group, you must make sure that the input > coordinates from the very beginning (that is, already in the > jobfile) are in perfect agreement with this symmetry. Then > Gaussian will adopt this symmetry, and the optimization > procedure will continue within that symmetry. So, if you are > convinced that your molecule possesses certain symmetry > properties, make sure that your input coordinates precisely > reflect this symmetry. > > In the present case, it is apparent from the input coordinates > of your jobfile that the compound in question is 2-methyl- > anilin. If you want this molecule to posses a plane of > symmetry, corresponding to the input configuration, you must > make sure that the coordinates for the two hydrogens in > positions no. 13 and 15 are symmetrized: > > H 2.583600 1.09939 0.89064 > H 2.583600 1.09939 -0.89064 > > and that the z-coordinate of the hydrogen in position 14 is > equal to zero: > > H 2.742198 -0.435063 0.00000 > > Then Gaussian will recognize a plane of symmetry, and > wavefunctions will be characterized according to the > irreducible representations of the Cs pointgroup. If you start > the calculation within this Cs geometry, the optimization will > continue within this symmetry, it cannot "break out". > > However, the assumption of Cs symmetry is probably not > realistic for 3-methyl-aninlin. The equilibrium geometry of > this compound would not be expected to have any symmetry > elements at all (apart from the identity operation). The > pyramidalization of the NH2 group will destroy the molecular > plane of symmetry. - Also the conformation of the methyl group > in your input geometry seems problematic. > > Jens >--< > > > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > JENS SPANGET-LARSEN Office: +45 4674 2710 > Department of Chemistry Fax: +45 4674 3011 > Roskilde University (RUC) Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget)at(ruc.dk > DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > From chemistry-request@ccl.net Wed Jul 2 06:56:04 2003 Received: from socrates.cc.uoi.gr (socrates.cc.uoi.gr [195.130.119.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h62Au3qe029016 for ; Wed, 2 Jul 2003 06:56:04 -0400 Received: from prokopis (pc159.chem.uoi.gr [195.130.116.159]) by socrates.cc.uoi.gr (8.9.3/8.9.3) with SMTP id NAA174547 for ; Wed, 2 Jul 2003 13:50:03 +0300 (EEST) Message-ID: <000f01c34088$84641fb0$9f7482c3@prokopis> From: "George Papamokos" To: Subject: Date: Wed, 2 Jul 2003 13:55:57 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000C_01C340A1.A98E3F50" 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_000C_01C340A1.A98E3F50 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Ed, In general, the accuracy of DFT under a basis set, depends on the = functional you are using and on the kind of species you are working on, plus the property you are seeking (DFT is an aproximate = method). Generally it is not improved with the basis set. Most articles I have read, use at least 6-31G*for every functional. If = you have decided your functional, look under what basis set it was = parametrized. I hope I helped. George Papamokos ----- Original Message ----- From: "Ed Brothers" To: Sent: Tuesday, July 01, 2003 12:17 AM Subject: CCL:Small basis set DFT. > Folks: > Has anyone ever published a discussion of the accuracy of DFT at > small basis sets? > > Ed. > Merz group. > Penn State. > > > -=3D This is automatically added to each message by mailing script = =3D- > To send e-mail to subscribers of CCL put the string CCL: on your = Subject: line > and send your message to: CHEMISTRY)at(ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the = maintainer: > Jan Labanowski, jkl)at(ccl.net (read about it on CCL Home Page) > = -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > ------=_NextPart_000_000C_01C340A1.A98E3F50 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Ed,
In general, the accuracy of DFT under a basis set, = depends on=20 the functional
you are using and on the kind of species you = are
working=20 on, plus the property you are seeking (DFT is an aproximate=20 method).
Generally it is not improved with the basis set.
Most = articles I=20 have read, use at least 6-31G*for every functional. If you
have = decided your=20 functional, look under what basis set it was parametrized.
 I = hope I=20 helped.

George Papamokos

----- Original Message = -----
From: "Ed=20 Brothers" <enb108)at(psu.edu>
To:=20 <chemistry)at(ccl.net>
Sent:=20 Tuesday, July 01, 2003 12:17 AM
Subject: CCL:Small basis set=20 DFT.


> Folks:
>     Has anyone = ever=20 published a discussion of the accuracy of DFT at
> small basis=20 sets?
>
> Ed.
> Merz group.
> Penn=20 State.
>
>
> -=3D This is automatically added to each = message by=20 mailing script =3D-
> To send e-mail to subscribers of CCL put the = string=20 CCL: on your Subject:
line
> and send your message to:  CHEMISTRY)at(ccl.net
>
> = Send your=20 subscription/unsubscription requests to:
CHEMISTRY-REQUEST)at(ccl.net>=20 HOME Page: http://www.ccl.net   |=20 Jobs Page: http://www.ccl.net/jobs
>
&= gt; If=20 your mail is bouncing from CCL.NET domain send it to the = maintainer:
> Jan=20 Labanowski,  jkl)at(ccl.net (read = about it on=20 CCL Home Page)
>=20 -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+<= BR>>
>
>
>
>
------=_NextPart_000_000C_01C340A1.A98E3F50-- From chemistry-request@ccl.net Wed Jul 2 01:36:52 2003 Received: from mail2.cc.huji.ac.il (outmail.cc.huji.ac.il [132.64.1.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h625apqe022609 for ; Wed, 2 Jul 2003 01:36:52 -0400 Received: from 127.0.0.1 (localhost.localdomain [127.0.0.1]) by mail2.cc.huji.ac.il (Postfix) with SMTP id E7BA940266; Wed, 2 Jul 2003 08:36:49 +0300 (IDT) Received: by mail2.cc.huji.ac.il (Postfix, from userid 31998) id C51DD401FE; Wed, 2 Jul 2003 08:36:49 +0300 (IDT) Received: from pob.huji.ac.il (pob.huji.ac.il [132.64.1.8]) by mail2.cc.huji.ac.il (Postfix) with ESMTP id 0DEA940283; Wed, 2 Jul 2003 08:36:44 +0300 (IDT) Received: from amiram13.md.huji.ac.il (amiram13.md.huji.ac.il [132.64.165.248]) by pob.huji.ac.il (Postfix) with ESMTP id B0AE9FAFD; Wed, 2 Jul 2003 08:36:44 +0300 (IDT) Content-Type: text/plain; charset="iso-8859-1" From: Boris Gorelik To: CCL Mailing List Subject: [SOLVED] CCL:Ambiguous rotation values Date: Wed, 2 Jul 2003 08:36:24 +0000 User-Agent: KMail/1.4.3 References: <200306291838.14918.bgbg)at(pob.huji.ac.il> In-Reply-To: <200306291838.14918.bgbg)at(pob.huji.ac.il> Cc: Rick Venable MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200307020836.24597.bgbg)at(pob.huji.ac.il> X-Spam-Status: No, hits=-105.9 required=5.8 tests=AWL,BAYES_10,EMAIL_ATTRIBUTION,IN_REP_TO,REFERENCES, REPLY_WITH_QUOTES,SIGNATURE_LONG_DENSE,USER_AGENT_KMAIL, USER_IN_WHITELIST autolearn=ham version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Tue, 1 Jul 2003 17:53:48 -0400 Rick Venable wrote: >It occurs to me that for a unit vector and it's inverse, and rotations >of A that differ by pi, you will get the same relative orientation. >Try just sampling A from 0 to pi Yes, that was one part of the problem, but that was not all. We changed the sampling of phi and theta (angles that define axis direction) to be from 0 to PI (thus limiting the axis direction to one hemisphere), but the problem was still present. Then we noted two points: 1. If A (the rotation angle) equals zero then every combination will result in the same rotation (or should I say lack of rotation) 2. If the direction of the rotation axis is parallel to Z (theta==0), for a given A angle, all phi values will result in the same rotation. Thanks for help -- Boris Gorelik -= ( 2*b || !(2*b)) That's the question =- Wed, 02/Jul/2003, 2 Tamuz 5763 ------------------------------------------------- ! Molecular Modelling Group ! ! Pharmacy School, Hadassa Faculty of medicine ! ! The Hebrew University of Jerusalem ! ! http://www.md.huji.ac.il/models/group.html ! ! !------------------------------------------------ From chemistry-request@ccl.net Tue Jul 1 23:42:42 2003 Received: from mx3.ust.hk (mx3.ust.hk [143.89.13.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h623geqe020231 for ; Tue, 1 Jul 2003 23:42:41 -0400 Received: from ust.hk (sqmail1.ust.hk [143.89.15.20]) by mx3.ust.hk (8.12.9/8.12.9) with SMTP id h623gbfm053253 for ; Wed, 2 Jul 2003 11:42:37 +0800 (HKT) Received: from 143.89.53.94 (SquirrelMail authenticated user chgy) by sqmail.ust.hk with HTTP; Wed, 2 Jul 2003 11:42:37 +0800 (HKT) Message-ID: <1761.143.89.53.94.1057117357.squirrel)at(sqmail.ust.hk> Date: Wed, 2 Jul 2003 11:42:37 +0800 (HKT) Subject: Counterpoise problem of Gaussian03 From: "GAO Yi" To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.8) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, I tried the Z-matrix and Cartesian coordinates in Gaussian98 and Gaussian03, but the results are wrong for Guassian98, while Gaussian03 can't compute the counterpoise corrections of the separate parts for all.Would you kindly give me some suggestions? Best Yi Gao Department of Chemistry, HKUST, HK Below is the results of Gaussian03 program: >> Input file (Z-matrix): >> %mem=100mb >> #p rb3lyp/6-31g(d) Counterpoise=2 >> >> test >> >> 0 1 0 1 0 1 >> C,0.0,0.0,0.0,1 >> C, 1, B1,1 >> C, 2, B2,1, A1,0,1 >> C, 3, B3,2, A2, 1, D1,0,1 >> S, 1, B4,2, A3, 3, D2,0,1 >> H, 1, B5,2, A4, 3, D3,0,1 >> H, 2, B6,1, A5, 5, D4,0,1 >> H, 3, B7,2, A6, 1, D5,0,1 >> H, 4, B8,3, A7, 2, D6,0,1 >> C, 1, R1,2, A8, 3, D7,0,2 >> C, 2, R1,1, A9,10, D8,0,2 >> C, 3, R1,2,A10, 1, D9,0,2 >> C, 4, R1,3,A11, 2,D10,0,2 >> S, 5, R1,1,A12, 2,D11,0,2 >> H,10,B14,1,A13, 2,D12,0,2 >> H,11,B15,2,A14, 1,D13,0,2 >> H,12,B16,3,A15, 2,D14,0,2 >> H,13,B17,4,A16, 3,D15,0,2 >> >> B1 1.367442 >> B2 1.429838 >> B3 1.367442 >> B4 1.736068 >> B5 1.081675 >> B6 1.084843 >> B7 1.084842 >> B8 1.081675 >> B14 1.081675 >> B15 1.084843 >> B16 1.084842 >> B17 1.081675 >> A1 112.744698 >> A2 112.744698 >> A3 111.502553 >> A4 128.421983 >> A5 123.322645 >> A6 123.932686 >> A7 128.421983 >> A8 90.000000 >> A9 90.000000 >> A10 90.000000 >> A11 90.000000 >> A12 90.000000 >> A13 90.000000 >> A14 90.000000 >> A15 90.000000 >> A16 90.000000 >> D1 0.000000 >> D2 0.000000 >> D3 180.000000 >> D4 180.000000 >> D5 180.000000 >> D6 180.000000 >> D7 -90.000000 >> D8 0.000000 >> D9 90.000000 >> D10 90.000000 >> D11 -90.000000 >> D12 -128.421983 >> D13 123.322645 >> D14 123.932686 >> D15 128.421983 >> >> R1 3.0 >> >> Output file: >> >> Symmetry A' KE= 5.487337134003D+02 >> Symmetry A" KE= 5.517851430966D+02 >> No NMR shielding tensors so no spin-rotation constants. >> Leave Link 601 at Tue Jul 1 10:10:08 2003, MaxMem= 13107200 cpu: >> 0.8 (Enter /usr/local/g03/l122.exe) >> Counterpoise: doing DCBS calculation for fragment 1 NewBq=T >> Leave Link 122 at Tue Jul 1 10:10:08 2003, MaxMem= 13107200 cpu: >> 0.0 (Enter /usr/local/g03/l301.exe) >> Basis read from rwf: (6D, 7F) >> No pseudopotential information found on rwf file. >> There are 87 symmetry adapted basis functions of A' symmetry. >> There are 87 symmetry adapted basis functions of A" symmetry. >> Integral buffers will be 262144 words long. >> Raffenetti 2 integral format. >> Two-electron integral symmetry is turned on. >> 174 basis functions, 360 primitive gaussians, 174 cartesian >> basis functio >> ns >> 22 alpha electrons 22 beta electrons >> nuclear repulsion energy 201.6692107959 Hartrees. >> IExCor= 402 DFT=T Ex=B+HF Corr=LYP ExCW=0 ScaHFX= 0.200000 >> ScaDFX= 0.800000 0.720000 1.000000 0.810000 >> IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 >> NAtoms= 18 NActive= 18 NUniq= 9 SFac= 5.66D+00 NAtFMM= 60 >> Big=F No density basis found on file 718. >> Leave Link 301 at Tue Jul 1 10:10:08 2003, MaxMem= 13107200 cpu: >> 0.0 (Enter /usr/local/g03/l302.exe) >> NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 >> NCelD= 1 >> NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. >> One-electron integrals computed using PRISM. >> One-electron integral symmetry used in STVInt >> NBasis= 174 RedAO= T NBF= 87 87 >> NBsUse= 174 1.00D-06 NBFU= 87 87 >> Precomputing XC quadrature grid using >> IXCGrd= 2 IRadAn= 0 IRanWt= -1 IRanGd= >> 0. NRdTot= 1114 NPtTot= 141812 NUsed= 146862 NTot= >> 146878 NSgBfM= 173 173 173 173. >> Leave Link 302 at Tue Jul 1 10:10:10 2003, MaxMem= 13107200 cpu: >> 1.8 (Enter /usr/local/g03/l303.exe) >> DipDrv: MaxL=1. >> Leave Link 303 at Tue Jul 1 10:10:11 2003, MaxMem= 13107200 cpu: >> 0.1 (Enter /usr/local/g03/l401.exe) >> Harris functional with IExCor= 402 diagonalized for initial guess. >> ExpMin= 1.17D-01 ExpMax= 2.19D+04 ExpMxC= 3.30D+03 IAcc=1 IRadAn= >> 1 Acc >> Des= 1.00D-06 >> HarFok: IExCor= 402 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 >> ScaDFX= 1.000000 1.000000 1.000000 1.000000 >> Spurious integrated density or basis function: >> NE= 44 NElCor= 0 El error=4.35D+01 rel=9.88D-01 >> Tolerance=1.00D-03 Shell 20 absolute error=3.21D-04 >> Tolerance=1.20D-02 Shell 20 signed error=3.21D-04 >> Tolerance=1.00D-01 Inaccurate quadrature in CalDSu. >> Error termination via Lnk1e in /usr/local/g03/l401.exe at Tue Jul 1 >> 10:10:14 2 >> 003. >> Job cpu time: 0 days 0 hours 4 minutes 30.1 seconds. From chemistry-request@ccl.net Wed Jul 2 06:07:24 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h62A7Nqe027989 for ; Wed, 2 Jul 2003 06:07:23 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h62A7Mka096458 for ; Wed, 2 Jul 2003 12:07:22 +0200 (CEST) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h62A7M4X023838; Wed, 2 Jul 2003 12:07:22 +0200 (MEST) Date: Wed, 2 Jul 2003 12:07:22 +0200 (MEST) From: Michel Petitjean Message-Id: <200307021007.h62A7M4X023838[at]ds10.itodys.jussieu.fr> To: chemistry[at]ccl.net Subject: CCL:Re: Ambiguous rotation values X-Antivirus: scanned by sophie at shiva.jussieu.fr To: CCL Mailing List Subject: CCL:Re: Ambiguous rotation values The relation between rotation matrix and axis+angle is usually get from the quaternionic parametrization of the rotation, rather than from the theta,phi,A system. When you set theta=0 and phi=any_phi_value in: a1x=sin(theta)*cos(phi), a2x=sin(theta)*sin(phi), a3x=cos(theta). then you get (0,0,1) as direction of the axis, although I presume that you would like to get independantly direction and angle. The quaternionic formulation is available from numerous textbooks and papers (e.g. J.Comput.Chem. 1995,16[1],80-90): having a unit vector (p,a,b,c), where p=cos(angle/2) and (a,b,c) is the direction, the rotation matrix R is: p^2+a^2-b^2-c^2 2*(ab-pc) 2*(ac+pb) R = 2*(ab+pc) p^2-a^2+b^2-c^2 2*(bc-pa) 2*(ac-pb) 2*(bc+pa) p^2-a^2-b^2+c^2 Conversely: p^2=(trace(R)+1)/4, and: a = ( R(3,2) - R(2,3) ) / 4p b = ( R(1,3) - R(3,1) ) / 4p c = ( R(2,1) - R(1,2) ) / 4p Note also than (p,a,b,c) and (-p,-a,-b,-c) are the smae, and that (a,b,c) is not a unit vector. Sampling 3D rotations is get from random isotropically 3D directions and random 2D angles (uniform law). Regularly tessellated figures are sometimes used to get equally spaced directions (e.g. from the vertices of the regular icosahedron), but random sampling is much satisfacory for high number of points. Michel Petitjean, Email: petitjean[at]itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean[at]ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Boris Gorelik wrote: >Dear All, >We are trying to sample all possible rotations of a rigid ligand in a discrete >3D space. We define the rotation using a1x, a2x, a3x and A, where >(a1x,a2x,a3x) is the unit vector in the direction of the axis and A is the >angle of rotation in radians. The unit vector is defined by two degrees of >freedom namely: spherical angles theta and phi, and is calculated from them. >We are using the rotate function from the BTL package >(http://bioinformatics.org/project/?group_id=184) >Unfortunately, sometimes we get identical conformations, while using different >input to the function. How can this problem can be avoided? > >Every idea will be highly appreciated > >PS >Some additional details: >we use discrete value for phi, theta and A: >000 >a1x=sin(theta)*cos(phi), >a2x=sin(theta)*sin(phi), >a3x=cos(theta). > >The rotate function is based on the following rotation matrix: >[cosA+a1x.a1x(1-cosA) -a3xsinA+a1a2(1-cosA) a2xsinA+a1xa3x(1-cosA) ] >[a3xsinA+a1xa2(1-cosA) cosA+a2xa2x(1-cosA) -a1xsinA+a2xa3x(1-cosA)] >[-a2xsinA+a3xa1x(1-cosA) a1xsinA+(1-cosA)a2xa3x cosA+(1-cosA)a3xa3x ] >-- >Boris Gorelik >-= ( 2*b || !(2*b)) That's the question =- >Sun, 29/Jun/2003, 30 Sivan 5763 >------------------------------------------------- >! Molecular Modelling Group ! >! Pharmacy School, Hadassa Faculty of medicine ! >! The Hebrew University of Jerusalem ! >! http://www.md.huji.ac.il/models/group.html ! >! >!------------------------------------------------ From chemistry-request@ccl.net Wed Jul 2 12:40:38 2003 Received: from mailhost2.tudelft.nl (mailhost2.tudelft.nl [130.161.180.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h62Gecqe005091 for ; Wed, 2 Jul 2003 12:40:38 -0400 Received: from 127.0.0.1 (localhost [127.0.0.1]) by rav.antivirus (Postfix) with SMTP id 3497B3D2 for ; Wed, 2 Jul 2003 18:40:37 +0200 (MEST) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (Postfix) with ESMTP id 214963D0 for ; Wed, 2 Jul 2003 18:40:37 +0200 (MEST) Received: from mail.dct.tudelft.nl (tnw-dct1.dct.tudelft.nl [130.161.196.201]) by listserv.tudelft.nl (8.12.8p1/8.12.8) with ESMTP id h62Geakl016530 for ; Wed, 2 Jul 2003 18:40:36 +0200 (MEST) Received: from TNW-DCT1/SpoolDir by mail.dct.tudelft.nl (Mercury 1.48); 2 Jul 03 18:40:36 +0200 Received: from SpoolDir by TNW-DCT1 (Mercury 1.48); 2 Jul 03 18:40:31 +0200 From: "Martijn Zwijnenburg" Organization: Delft University of Technology (TNW-DCT) To: chemistry*at*ccl.net Date: Wed, 02 Jul 2003 18:40:24 +0200 MIME-Version: 1.0 Subject: ccl: 6-31G** basis-set in G98 for Ge Message-ID: <3F032710.26615.2AF4C9FA@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.11) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Hi, I'm wondering were the 6-31G** basis-set for Ge in G98 originates from? Since I can only find 6-31G** basis-sets upto Zn at for instance the EMSL Basis Set Library site. Furthermore, it doesn't really strike me as 6-31G** (more functions, no f functions for polarization, see below). Anybody a guess? Thanx in advance, Martijn Zwijnenburg **** 18 0 S 8 1.00 0.4890000000D+06 0.2220000000D-03 0.7310000000D+05 0.1728000000D-02 0.1664000000D+05 0.8950000000D-02 0.4742000000D+04 0.3590500000D-01 0.1569000000D+04 0.1128400000D+00 0.5770000000D+03 0.2874800000D+00 0.2290000000D+03 0.4344900000D+00 0.9481000000D+02 0.3068300000D+00 S 2 1.00 0.2922000000D+02 0.4775900000D+00 0.1245000000D+02 0.1114450000D+01 S 1 1.00 0.3642000000D+01 0.1000000000D+01 S 1 1.00 0.1502000000D+01 0.1000000000D+01 S 1 1.00 0.2462000000D+00 0.1000000000D+01 S 1 1.00 0.9209000000D-01 0.1000000000D+01 P 6 1.00 0.3596000000D+04 0.1442000000D-02 0.8437000000D+03 0.1244200000D-01 0.2662000000D+03 0.6469400000D-01 0.9828000000D+02 0.2186650000D+00 0.3993000000D+02 0.3933500000D+00 0.1714000000D+02 0.4345300000D+00 P 3 1.00 0.7157000000D+01 0.2499750000D+00 0.3068000000D+01 0.4693800000D+00 0.1246000000D+01 0.2889600000D+00 P 1 1.00 0.2795000000D+00 0.1000000000D+01 P 1 1.00 0.8340000000D-01 0.1000000000D+01 D 5 1.00 0.7018000000D+02 0.2877000000D-01 0.2007000000D+02 0.1552500000D+00 0.7059000000D+01 0.3681400000D+00 0.2553000000D+01 0.4657800000D+00 0.8301000000D+00 0.2864800000D+00 D 1 1.00 0.2020000000D+00 0.1000000000D+01 **** ---------------------------------------------------------------------- --- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg*at*tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@ccl.net Tue Jul 1 21:10:40 2003 Received: from GWIA.HSC.WVU.EDU (gateway.hsc.wvu.edu [157.182.105.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h621Adqe017317 for ; Tue, 1 Jul 2003 21:10:40 -0400 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Tue, 01 Jul 2003 21:10:39 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Tue, 01 Jul 2003 21:10:11 -0400 From: "Peter Gannett" To: Subject: Re: CCL:insightII/discover vs CHARMM Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline Yao-Ying: I am not a CHARMM user but do use a similar program - Amber. I have also used Insight. There are pros/cons to either and it will depend on your circumstances. However, some pros/cons that come to mind are: Insight costs a lot more than Charmm if you are at an academic institution (ca $20,000 for Insight, less than $1000 for Charmm, last I checked, $600). Insight only runs in a serial environment, charm, I believe, runs in either a serial or parallel mode. Insight will offer tech service, charmm doesn't directly. However, I have not been impressed with Insight's tech service and listserves for charmm are free and probably more helpful. Insight has excellent graphics. Both will solve protein/dna problems. Which is better for either problem is debatable. Here's a third option to consider. Get NAMD/VMD. These programs will do anything that Insight/CHARMM/Amber will do but NAMD/VMD are free. Pete Gannett >>> Yao-Ying Chien 07/01/03 20:04 PM >>> Hi, Can someone tell me the pro's and con's of insightII/discover vs CHARMM? I have used insightII/discover, but most people here seem to use CHARMM. Wonder if you guys can explain for me the difference, in terms of the pro's and con's? And if any reasons I should switch to CHARMM? URL's discussing these are appreciated too. Thanks, Yao -= This is automatically added to each message by mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY$at$ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST$at$ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl$at$ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed Jul 2 13:19:35 2003 Received: from web15203.mail.bjs.yahoo.com (web15203.mail.bjs.yahoo.com [202.3.77.133]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h62HJSqe005943 for ; Wed, 2 Jul 2003 13:19:30 -0400 Message-ID: <20030702171902.3682.qmail)at(web15203.mail.bjs.yahoo.com> Received: from [202.102.164.163] by web15203.mail.bjs.yahoo.com via HTTP; Thu, 03 Jul 2003 01:19:02 CST Date: Thu, 3 Jul 2003 01:19:02 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: Re: About octanol/water partition coefficient (Kow) To: CCL In-Reply-To: <20030701153707.19650.qmail)at(web15202.mail.bjs.yahoo.com> MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit I should make it more clear. I hope to know methods that could be used to predict the Kow of two or more organic chemicals that are solved in the octanol/water system at the same time. I mean I hope to know the Kow of a mixture consisting of two or more organic chemicals if I know the fraction of each chemicals. Many thanks to the response to my previous questions. Regards, Jinsong --- Jinsong Zhao : > Dear all, > > As you know, now the octanol/water partition > coefficient, i.e., Kow, could be calculated using > many > programs. > > However, those softwares just give the Kow of a > sigle > organic chemical in the octanol/water system. I am > very interested in the prediction for the Kow of two > or more organic chemicals in such system. > > Is it possible to do the prediction? Any suggestions > or comments will be welcome! > > Thanks in advance! > > Regards, > > Jinsong > _________________________________________________________ Do You Yahoo!? MxA55DZ9JM#:UfGi;9JG7EW]#? http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/netlove From chemistry-request@ccl.net Wed Jul 2 01:28:55 2003 Received: from kdmail2.netcologne.de (kdmail2.netcologne.de [194.8.194.86]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h625Stqe022517 for ; Wed, 2 Jul 2003 01:28:55 -0400 Received: from cosmologic.de (xdsl-195-14-220-71.netcologne.de [195.14.220.71]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 2.9.3.5) with ESMTP id ABS81320 (AUTH klamt*at*cosmologic.de); Wed, 2 Jul 2003 07:28:51 +0200 (CEST) Message-ID: <3F026D90.4050306*at*cosmologic.de> Date: Wed, 02 Jul 2003 07:28:48 +0200 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Jinsong Zhao , CHEMISTRY Subject: Re: CCL:About octanol/water partition coefficient (Kow) References: <20030701153707.19650.qmail*at*web15202.mail.bjs.yahoo.com> Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: 7bit To be honest, I do not exactly understand what you are looking for. But our COSMOtherm program (see www.cosmologic.de) is able to predict general partition coefficients of almost arbitrary organic compounds between almost arbitrary phases at variable temperature, just based on quantum chemical calculations. Andreas Jinsong Zhao wrote: >Dear all, > >As you know, now the octanol/water partition >coefficient, i.e., Kow, could be calculated using many >programs. > >However, those softwares just give the Kow of a sigle >organic chemical in the octanol/water system. I am >very interested in the prediction for the Kow of two >or more organic chemicals in such system. > >Is it possible to do the prediction? Any suggestions >or comments will be welcome! > >Thanks in advance! > >Regards, > >Jinsong > >_________________________________________________________ >Do You Yahoo!? >MxA55DZ9JM#:UfGi;9JG7EW]#? >http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/netlove > > >-= This is automatically added to each message by mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY*at*ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST*at*ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl*at*ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt*at*cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@ccl.net Wed Jul 2 10:28:47 2003 Received: from mx4.trentu.ca (mx4.trentu.ca [192.75.12.5]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h62ESlqe001890 for ; Wed, 2 Jul 2003 10:28:47 -0400 Received: (qmail 13744 invoked by uid 504); 2 Jul 2003 14:28:46 -0000 Received: from elewars-.at.-trentu.ca by mx4.trentu.ca by uid 501 with qmail-scanner-1.16 ( Clear:. Processed in 0.026949 secs); 02 Jul 2003 14:28:46 -0000 X-Qmail-Scanner-Mail-From: elewars-.at.-trentu.ca via mx4.trentu.ca X-Qmail-Scanner: 1.16 (Clear:. Processed in 0.026949 secs) Received: from unknown (HELO trentu.ca) (209.42.101.30) by mx4.trentu.ca with SMTP; 2 Jul 2003 14:28:46 -0000 Message-ID: <3F02ECDD.D642E01A-.at.-trentu.ca> Date: Wed, 02 Jul 2003 10:31:57 -0400 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry-.at.-ccl.net Subject: re DFT and small basis sets Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 2003 July 1 Re "Has anyone ever published a discussion of the accuracy of DFT at small basis sets?" I'm not sure just what you consider small (most workers now would likely say that 6-31G* is small), but DFT calculations are known to be saturated by basis functions more quickly than are ab initio calculations. Here are three refs: 1) "Once the double split-valence level is reached, further improvement in basis set quality offers little in the way of structutal or energetic improvement." G. N. Merrill, S. Gronert, and S. R. Kass. J Phys Chem, 1997, _101_, 204. 2) "Our results also show that B3LYP calculations converge rapidly with increasing basis set size and that the cost-to-benefit- ratio is optimal at the 6-31G* basis set level. 6-31G* will be the basis set of choice in B3LYP calculations on much larger molecules [than C4H6O2]." P. J. Stephens, F. J. Devlin, C. F. Chablowski, and M. J. Frisch, J Phys Chem, 1994, _98_, 11623, and refs therein. 3) In defiance of tradition, the unequivocally small 3-21G(*) set has been used to optimize carbene geometries: H. M. Muchall, N. H. Werstiuk, and B. Chodhurry, Can J Chem, 1998, _76_, 221. (You my also find some useful info in E. Lewars, "Computational Chemistry", Kluwer, 2003; section 7.3.2.2). E. Lewars ======== Ed Brothers wrote: > Folks: > Has anyone ever published a discussion of the accuracy of DFT at > small basis sets? > > Ed. > Merz group. > Penn State. > From chemistry-request@ccl.net Tue Jul 1 22:32:00 2003 Received: from web41707.mail.yahoo.com (web41707.mail.yahoo.com [66.218.93.124]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h622W0qe018534 for ; Tue, 1 Jul 2003 22:32:00 -0400 Message-ID: <20030702023159.84337.qmail(at)web41707.mail.yahoo.com> Received: from [130.127.153.188] by web41707.mail.yahoo.com via HTTP; Tue, 01 Jul 2003 19:31:59 PDT Date: Tue, 1 Jul 2003 19:31:59 -0700 (PDT) From: Vivek Raut Reply-To: vraut(at)clemson.edu Subject: CCL: Tinker for parallel?? To: CHEMISTRY(at)ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-940196972-1057113119=:84023" --0-940196972-1057113119=:84023 Content-Type: text/plain; charset=us-ascii Can Tinker be used for parallel processing, if yes then how efficient is it than say GROMACS?.. if no , then how likely this feature will be incorporated in Tinker?? - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Vivek Raut Graduate Research Assistant Dept. of Bioengineering Clemson University, SC- 29631. Email:vraut(at)clemson.edu Phone: 864-650-1431 --------------------------------- Do you Yahoo!? SBC Yahoo! DSL - Now only $29.95 per month! --0-940196972-1057113119=:84023 Content-Type: text/html; charset=us-ascii
Can Tinker be used for parallel processing, if yes then how efficient is it than say GROMACS?.. if no , then how likely this feature will be incorporated in Tinker??
 


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Vivek Raut
Graduate Research Assistant
Dept. of Bioengineering
Clemson University, SC- 29631.
Email:vraut(at)clemson.edu
Phone: 864-650-1431

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