From owner-chemistry@ccl.net Mon Sep 19 00:50:03 2005 From: "CCL" To: CCL Subject: CCL: W:ChemScore Message-Id: <-29221-050918234853-29460-ypVT4zBISehoQe4g3/MdLQ||server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 18 Sep 2005 19:30:19 -0700 MIME-Version: 1.0 Sent to CCL by: Mark Thompson [mark||arguslab.com] --Replace strange characters with the "at" sign to recover email address--. Dear Robert, Would you summarize for the CCL group when you get your information? Cheers, Mark Thompson mark||arguslab.com CCL wrote: >Sent to CCL by: "Robert Jorissen" [jorissen*o*umbi.umd.edu] > >--Replace strange characters with the "at" sign to recover email address--. > >Hi > >I am currently implementing the ChemScore function of Eldridge et al., 1997 (JCAMD 11:425-445) for scoring docked conformations as generated by our in-house docking program, and would like to hear from other people who have implemented ChemScore. In particular, I would like to know what set of vdW radii are used; the radii are required for calculating the lipophilic contribution to this scoring function. Additionally, I would like to know of any example data that would allow me to assess whether I have implemented the individual terms (hydrogen bond, lipophilic, metal and rotatable bond terms) correctly. > >Any responses would be appreciated. > >Robert Jorissen >Center for Advanced Research in Biotechnology> > > > > > > -- ---------------------------- Mark Thompson mark||arguslab.com http://www.arguslab.com ---------------------------- From owner-chemistry@ccl.net Mon Sep 19 03:57:16 2005 From: "CCL" To: CCL Subject: CCL: spin contamination and S**2 Message-Id: <-29222-050919032853-26444-pzYVOMTxrbtVkkD1ukl2+g[#]server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-2-631293012 Date: Mon, 19 Sep 2005 09:27:44 +0200 Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Marcel Swart [m.swart[#]few.vu.nl] --Replace strange characters with the "at" sign to recover email address--. --Apple-Mail-2-631293012 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Hello Telkuni, yes, "S squared" of 0.5 for a singlet, and 1.2 for a doublet are spin =20= contaminated. There are some correction schemes available to "project out" the pure =20= state; we've recently reported some results for iron porphyrins in: J. Phys. Chem. A 2005, 109, 3411 On Sep 18, 2005, at 10:28 PM, CCL wrote: > > Sent to CCL by: "Telkuni Tsuru" [telkuni^^venus.dti.ne.jp] > > --Replace strange characters with the "at" sign to recover email =20 > address--. > > Hello, Callers. > > I like to ask the relationship between the spin contamination and > S**2 value. > > As mentioned before, S**2 shows the spin state, singlet(=3D0 [+/- = 10%]), > doublet (=3D0.75 [+/- 10%]), triplet (=3D2.0 [+/- 10%]), etc. When one > molecule's multiplicity is singlet and its S**2 is 0.5, can I say that > the molecule has spin contamination ? > And the same manner, the multiplicity is doublet and its S**2 is 1.2, > can I say that the molecule has spin contamination too ? > > (What should I call "S**2"? Is it "S star 2"?) > > All responses, I will appreciate. > I will summarize them and send to CCL. > > > Thanks in advance > --------------------------------------------------- > Telkuni Tsuru telkuni[#]venus.dti.ne.jp > > > > -=3D This is automatically added to each message by the mailing script = =3D- > To send e-mail to subscribers of CCL put the string CCL: on your =20 > Subject: line> > Send your subscription/unsubscription requests to: =20 > CHEMISTRY-REQUEST[#]ccl.net> > If your is mail bouncing from ccl.net domain due to spam filters, =20 > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-=20= > +-+ > > > > =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart[#]few.vu.nl Web http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-2-631293012 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 Hello Telkuni, yes, "S squared" of 0.5 for a singlet, and 1.2 for a doublet are spin contaminated. There are some correction schemes available to "project out" the pure state; we've recently reported some results for iron porphyrins in: J. Phys. Chem. A 2005, 109, 3411 On Sep 18, 2005, at 10:28 PM, CCL wrote: Sent to CCL by: "Telkuni Tsuru" [telkuni^^venus.dti.ne.jp] --Replace strange characters with the "at" sign to recover email address--. Hello, Callers. I like to ask the relationship between the spin contamination and=20 S**2 value. As mentioned before, S**2 shows the spin state, singlet(=3D0 [+/- 10%]),=20= doublet (=3D0.75 [+/- 10%]), triplet (=3D2.0 [+/- 10%]), etc. When one=20= molecule's multiplicity is singlet and its S**2 is 0.5, can I say that=20= the molecule has spin contamination ? And the same manner, the multiplicity is doublet and its S**2 is 1.2,=20 can I say that the molecule has spin contamination too ? (What should I call "S**2"? Is it "S star 2"?) All responses, I will appreciate.=20 I will summarize them and send to CCL. Thanks in advance --------------------------------------------------- Telkuni Tsuru telkuni[#]venus.dti.ne.jp -=3D This is automatically added to each message by the mailing script = =3D-Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[#]ccl.net=20 HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs=20use the Web based form from CCL Home Page=20= Helvetica=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96 = Papyrusdr. Marcel Swart = Papyrus = OsakaTheoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart[#]few.vu.nl Web http://www.few.vu.nl/~swart = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-2-631293012-- From owner-chemistry@ccl.net Mon Sep 19 08:24:39 2005 From: "CCL" To: CCL Subject: CCL: make: *** [g98] Error 2 Message-Id: <-29223-050919082350-30945-3bMyOfKH7ok6n7Bjyh5K8g|"|server.ccl.net> X-Original-From: Alexander Martins Silva Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 19 Sep 2005 09:29:00 -0300 MIME-Version: 1.0 Sent to CCL by: Alexander Martins Silva [alex.msilva|"|uol.com.br] --Replace strange characters with the "at" sign to recover email address--. Hi everyone, I'm trying to compile the gaussian 98 at FC 4 but I have the following error: make[1]: Leaving directory `/usr/local/src/abinitio/g98' pgf77 -O2 -malign-double -o g98 ml0.o util.so pgf77-Warning-Unknown switch: -malign-double /usr/bin/ld: g98: hidden symbol `fstat' in /usr/lib/libc_nonshared.a(fstat.oS) is referenced by DSO /usr/bin/ld: final link failed: Nonrepresentable section on output make: *** [g98] Error 2 endif What it means? How can fix it? I have the same problem with gcc. Thanks in advance, Alexander. From owner-chemistry@ccl.net Mon Sep 19 08:50:02 2005 From: "CCL" To: CCL Subject: CCL: Gaussian - partial optimization Message-Id: <-29224-050919084856-9302-VuoLzDvpiTG3C5WXY7inMQ : server.ccl.net> X-Original-From: "Tomasz Grabarkiewicz" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0051_01C5BD29.349E3720" Date: Mon, 19 Sep 2005 14:48:32 +0200 MIME-Version: 1.0 Sent to CCL by: "Tomasz Grabarkiewicz" [grabar : man.poznan.pl] --Replace strange characters with the "at" sign to recover email address--. This is a multi-part message in MIME format. ------=_NextPart_000_0051_01C5BD29.349E3720 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable Hi, I'm trying to establish a mutual orientation of two hydroxyl groups in a = dimeric system (Gaussian). Unfortunately, when I perform a partial optimization of these groups the = relative distance beetwen two molecules is also changing. What could be done to optimize only hydroxyls while keeping the rest of = the system in its initial coordinates? ------=_NextPart_000_0051_01C5BD29.349E3720 Content-Type: text/html; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable
Hi,
I'm trying to establish a mutual = orientation=20 of two hydroxyl groups in a dimeric system  = (Gaussian).
Unfortunately, when I perform a partial = optimization of these groups the relative distance beetwen two = molecules is=20 also changing.
What could be done = to optimize only=20 hydroxyls while keeping the rest of the system in its = initial=20 coordinates?
------=_NextPart_000_0051_01C5BD29.349E3720-- From owner-chemistry@ccl.net Mon Sep 19 08:53:55 2005 From: "CCL" To: CCL Subject: CCL: spin contamination and S**2 Message-Id: <-29225-050919033853-26824-IL2YnwvD7VMXRnKlS2CzCA()server.ccl.net> X-Original-From: "Xavier ASSFELD" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-2022-jp" Date: Mon, 19 Sep 2005 09:01:31 +0200 MIME-Version: 1.0 Sent to CCL by: "Xavier ASSFELD" [Xavier.Assfeld()cbt.uhp-nancy.fr] --Replace strange characters with the "at" sign to recover email address--. Hi, for S**2 pronounce "S squared" (S multiplied by S). It is the expectation value of the total spin operator. If for a wavefunction of a singlet you get a S**2 value greater than 0 then it is spin contaminated. Spin contamination can only arises with states of higher multiplicity and of the same parity (odd or even) than the desired state. Hope this helps. ...Xav Pr. Xavier Assfeld Xavier.Assfeld()cbt.uhp-nancy.fr Chimie et Biochimie theoriques T: (33) 3 83 68 43 82 Faculte des Sciences F: (33) 3 83 68 43 71 54506 Vandoeuvre, France http://www.cbt.uhp-nancy.fr X> -----Message d'origine----- X> De?: owner-chemistry()ccl.net [mailto:owner-chemistry()ccl.net] X> Envoye?: dimanche 18 septembre 2005 22:29 X> A?: Assfeld, Xavier X> Objet?: CCL: spin contamination and S**2 X> X> X> X> Sent to CCL by: "Telkuni Tsuru" [telkuni^^venus.dti.ne.jp] X> X> --Replace strange characters with the "at" sign to recover email X> address--. X> X> Hello, Callers. X> X> I like to ask the relationship between the spin contamination and X> S**2 value. X> X> As mentioned before, S**2 shows the spin state, singlet(=0 [+/- 10%]), X> doublet (=0.75 [+/- 10%]), triplet (=2.0 [+/- 10%]), etc. When one X> molecule's multiplicity is singlet and its S**2 is 0.5, can I say that X> the molecule has spin contamination ? X> And the same manner, the multiplicity is doublet and its S**2 is 1.2, X> can I say that the molecule has spin contamination too ? X> X> (What should I call "S**2"? Is it "S star 2"?) X> X> All responses, I will appreciate. X> I will summarize them and send to CCL. X> X> X> Thanks in advance X> --------------------------------------------------- X> Telkuni Tsuru telkuni()venus.dti.ne.jp X> X> X> XX> To send e-mail to subscribers of CCL put the string CCL: on your X> Subject: line XX> X> Send your subscription/unsubscription requests to: X> CHEMISTRY-REQUEST()ccl.net XX> XXXX> X> X> From owner-chemistry@ccl.net Mon Sep 19 10:14:38 2005 From: "CCL" To: CCL Subject: CCL: Gaussian - partial optimization Message-Id: <-29226-050919101244-23195-9HGAgNGX9ipmoLHTCIgmKw[]server.ccl.net> X-Original-From: Joslyn Y Kravitz Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 19 Sep 2005 10:12:35 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Joslyn Y Kravitz [jyudenfr[]umich.edu] --Replace strange characters with the "at" sign to recover email address--. You should define your coordinates using internal rather than cartesian coordinates. If you define the distance between the molecules as one of the bond lengths then you can freeze that bond length and the two molecules should stay put. In fact, you can freeze all coordinates except for the atoms in the hydroxyl groups. Joslyn Kravitz On Mon, 19 Sep 2005, CCL wrote: > Hi, > I'm trying to establish a mutual orientation of two hydroxyl groups in > a dimeric system (Gaussian). > Unfortunately, when I perform a partial optimization of these groups the > relative distance beetwen two molecules is also changing. > What could be done to optimize only hydroxyls while keeping the rest of > the system in its initial coordinates? From owner-chemistry@ccl.net Mon Sep 19 10:27:31 2005 From: "CCL" To: CCL Subject: CCL: Winter School in Theoretical Chemistry, "Nanophotonics" Message-Id: <-29227-050919102201-29217-0aIcy8BCDjCpfpE0JeUA6A:+:server.ccl.net> X-Original-From: Mikael Johansson Content-Transfer-Encoding: 8bit Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Date: Mon, 19 Sep 2005 17:21:55 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson:+:helsinki.fi] --Replace strange characters with the "at" sign to recover email address--. Hello All! It is soon time again for the annual Winter School in Theoretical Chemistry, traditionally held at the University of Helsinki, Finland, this year between December 7 and 9. The School is free of charge, but participants are asked to kindly register by November 15th! For full information, see the home page of the School: http://www.chem.helsinki.fi/Info/WinterSchool/ws2005.html Topic: Nanophotonics Speakers: Filipp Furche, "Time-Dependent Density-Functional Theory: Gradients and Franck-Condon Shifts" Christof Hättig, "The CC2 Method: Parallel Implementation and Applications on Nanomolecules" Markku Leskelä, "The Atomic Layer Deposition Method: Thin Films and Other Nanostructured Materials" Jeppe Olsen, "CC and CI methods for Electron-Hole Systems: Applications on Semiconductor Quantum Dots" Sergei Tretiak, "Electronic excitations and photodynamics in conjugated polymers and carbon nanotubes" "Adiabatic and nonadiabatic excited state dynamics in molecular aggregates" "Nonlinear optical response of organic electronic materials" "Electronic structure and interactions in colloidal quantum dots and their assemblies" Artur Zrenner, "Optical Spectroscopy of Single Quantum-Dot System" Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson:+:helsinki.fi http://www.helsinki.fi/~mpjohans/ Phone: +358-9-191 50181 FAX : +358-9-191 50169 From owner-chemistry@ccl.net Mon Sep 19 11:50:27 2005 From: "CCL" To: CCL Subject: CCL: Problem freezing atoms with gaussian Message-Id: <-29228-050919113536-25029-IkdSsI0o7bIbaeY2FfAFuw() server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 19 Sep 2005 16:36:43 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc() iiqab.csic.es] --Replace strange characters with the "at" sign to recover email address--. Dear CClers, I am trying to perform an optimisation with gaussian having some atomic positions fixed. I use Opt=AddRedundant and then the list of atoms: 4 F 5 F 23 F etc. After the first step, and 100 iterationsof the kind: Iteration 6 RMS(Cart)= 0.14928401 RMS(Int)= 0.40589165 Iteration 7 RMS(Cart)= 0.14928401 RMS(Int)= 0.32910240 Iteration 8 RMS(Cart)= 0.14928401 RMS(Int)= 0.25609186 etc the gaussian output gives: "Curvilinear Step not converged" and stops. I have two questions. First, on the theoretical side, why does gaussian need to iteratively solve a set of equations to fix the position of the atoms? I understand that this is necessary for non-linear constraints such as distances or angles, but why for fixing cartesian coordinates? Is it because in redundant internal coordinates the atomic coordinates are not linearly related? And second, can I increase the maximum number of iterations to solve this system of equations? The default is 100 and I've looked into the Opt options and some IOp's and couldn't find anything. The system is quite large, but I do not see why fixing a set of atomic positions can lead to a unresolvable system. The set of constraints does not seem incompatible to me. Alternatively, is there a different way to fix some cartensian atomic positions? Thanks for your consideration, Ramon From owner-chemistry@ccl.net Mon Sep 19 13:52:17 2005 From: "CCL" To: CCL Subject: CCL: Cleaning up dusty deck fortran and converting to C/C++ Message-Id: <-29229-050919132237-22399-Y9sSeX/zCIETYgGBO1XmDA%a%server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 19 Sep 2005 12:20:43 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel%a%attglobal.net] --Replace strange characters with the "at" sign to recover email address--. Hello! I have some old fortran I would like to convert to C.. Have used F2C on an example code, which had me go back and clean up the fortran first.. not a bad thing. Are there any utilities that would take a dusty fortran deck and clean it up on its own... i.e. remove unused variables, and the like, for example? I have a 40,000 line F77 code I would like also to run in C. Many thanks, John McKelvey From owner-chemistry@ccl.net Mon Sep 19 14:32:10 2005 From: "CCL" To: CCL Subject: CCL: Gaussian - partial optimization Message-Id: <-29234-050919115142-30778-95JepoXYlM8UaMVAoewMww\a/server.ccl.net> X-Original-From: "Shobe, David" content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----=_NextPartTM-000-1034fdd5-7b9d-4912-a4c5-2428ee76a112" Date: Mon, 19 Sep 2005 11:50:02 -0400 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe\a/sud-chemieinc.com] --Replace strange characters with the "at" sign to recover email address--. This is a multi-part message in MIME format. ------=_NextPartTM-000-1034fdd5-7b9d-4912-a4c5-2428ee76a112 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5BD31.CC2686B2" ------_=_NextPart_001_01C5BD31.CC2686B2 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable It might be a matter of what exactly you did to freeze the non-hydroxyl = atoms...especially if the hydroxyl groups are the only contact between = the two molecules. If you freeze their cartesian coordinates of the = non-hydroxyl atoms (instead of internal coordinates like bond lengths = and angles), maybe that will fix the problem. --David Shobe, Ph.D., M.L.S.=20 S=FCd-Chemie, Inc.=20 phone (502) 634-7409=20 fax (502) 634-7724=20 Don't bother flaming me: I'm behind a firewall.=20 _____ =20 > From: owner-chemistry\a/ccl.net [mailto:owner-chemistry\a/ccl.net]=20 Sent: Monday, September 19, 2005 8:49 AM To: Shobe, David Subject: CCL: Gaussian - partial optimization Hi, I'm trying to establish a mutual orientation of two hydroxyl groups in a = dimeric system (Gaussian). Unfortunately, when I perform a partial optimization of these groups the = relative distance beetwen two molecules is also changing. What could be done to optimize only hydroxyls while keeping the rest of = the system in its initial coordinates?=20 ------_=_NextPart_001_01C5BD31.CC2686B2 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
It might be a matter of what exactly you = did to freeze=20 the non-hydroxyl atoms...especially if the hydroxyl groups are the = only=20 contact between the two molecules.  If you freeze their cartesian=20 coordinates of the non-hydroxyl atoms (instead of internal coordinates = like bond=20 lengths and angles), maybe that will fix the = problem.

--David Shobe, Ph.D., M.L.S. =
S=FCd-Chemie, Inc.
phone=20 (502) 634-7409
fax (502) = 634-7724

Don't bother flaming me: I'm behind a=20 firewall.


From: owner-chemistry\a/ccl.net=20 [mailto:owner-chemistry\a/ccl.net]
Sent: Monday, September 19, = 2005=20 8:49 AM
To: Shobe, David
Subject: CCL: Gaussian - = partial=20 optimization

Hi,
I'm trying to establish a mutual = orientation=20 of two hydroxyl groups in a dimeric system  = (Gaussian).
Unfortunately, when I perform a partial = optimization of these groups the relative distance beetwen two = molecules is=20 also changing.
What could be done = to optimize only=20 hydroxyls while keeping the rest of the system in its = initial=20 coordinates?
------_=_NextPart_001_01C5BD31.CC2686B2-- ------=_NextPartTM-000-1034fdd5-7b9d-4912-a4c5-2428ee76a112-- From owner-chemistry@ccl.net Mon Sep 19 14:32:10 2005 From: "CCL" To: CCL Subject: CCL: Problem freezing atoms with gaussian Message-Id: <-29232-050919131721-21834-cd5HlFToq/gZKXv2V06osQ:+:server.ccl.net> X-Original-From: Ben Sattelle Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format="flowed" Date: Mon, 19 Sep 2005 17:37:44 +0100 MIME-Version: 1.0 Sent to CCL by: Ben Sattelle [ben.sattelle:+:postgrad.manchester.ac.uk] --Replace strange characters with the "at" sign to recover email address--. > Alternatively, is there a different way to fix some > cartensian atomic positions? i use -1, see ... http://www.ccl.net/cgi-bin/ccl/message.cgi?2001+08+06+008 ben. From owner-chemistry@ccl.net Mon Sep 19 14:32:10 2005 From: "CCL" To: CCL Subject: CCL: Gaussian - partial optimization Message-Id: <-29230-050919110020-14297-kHFpkl7C2Iv+RIxPaBmfiw|"|server.ccl.net> X-Original-From: "d w" Content-Type: text/plain; format=flowed Date: Mon, 19 Sep 2005 14:11:36 +0000 Mime-Version: 1.0 Sent to CCL by: "d w" [wangdq2100|"|hotmail.com] --Replace strange characters with the "at" sign to recover email address--. hi, i didn't ever do such calculations, so my advice here is only for your reference and not sure it works: 1. if your molecule is not so large, try using "modredun" to fix the part as your want; 2. if molecule is too large, the method seems stupid. i remember there is a "constant" part in gaussian input file following "variable" part. so pls. prepare your input structure in the form of internal coordinate and move the parameter of the part you want to fix to the "constant" block. maybe you need care the ordering of the atoms in your molecule. good luck. wang >From: "CCL" >Reply-To: "CCL Subscribers" >To: "Wang, Dongqi " >Subject: CCL: Gaussian - partial optimization >Date: Mon, 19 Sep 2005 14:48:32 +0200 > >Hi, >I'm trying to establish a mutual orientation of two hydroxyl groups in a >dimeric system (Gaussian). >Unfortunately, when I perform a partial optimization of these groups the >relative distance beetwen two molecules is also changing. >What could be done to optimize only hydroxyls while keeping the rest of the >system in its initial coordinates? From owner-chemistry@ccl.net Mon Sep 19 14:32:10 2005 From: "CCL" To: CCL Subject: CCL: spin contamination and S**2 Message-Id: <-29233-050919111324-17045-QuKSqZxmP6eNBtpAg4VqBg:_:server.ccl.net> X-Original-From: "d w" Content-Type: text/plain; format=flowed Date: Mon, 19 Sep 2005 14:23:03 +0000 Mime-Version: 1.0 Sent to CCL by: "d w" [wangdq2100:_:hotmail.com] --Replace strange characters with the "at" sign to recover email address--. Dear Telkuni, according to my understanding, you can compare the S**2 (S Square) value with the scheme of S(S+1). if they are not equal, generally it's safe for you to say your calculation has spin contamination. according to this scheme, S**2 is 0 for singlet and 0.75 for doublet. i remember there is topic in Young's webpage. you can find the link from CCL homepage. good luck. wang >From: "CCL" >Reply-To: "CCL Subscribers" >To: "Wang, Dongqi " >Subject: CCL: spin contamination and S**2 >Date: Mon, 19 Sep 2005 05:28:49 +0900 > > >Sent to CCL by: "Telkuni Tsuru" [telkuni^^venus.dti.ne.jp] > >--Replace strange characters with the "at" sign to recover email address--. > >Hello, Callers. > >I like to ask the relationship between the spin contamination and >S**2 value. > >As mentioned before, S**2 shows the spin state, singlet(=0 [+/- 10%]), >doublet (=0.75 [+/- 10%]), triplet (=2.0 [+/- 10%]), etc. When one >molecule's multiplicity is singlet and its S**2 is 0.5, can I say that >the molecule has spin contamination ? >And the same manner, the multiplicity is doublet and its S**2 is 1.2, >can I say that the molecule has spin contamination too ? > >(What should I call "S**2"? Is it "S star 2"?) > > All responses, I will appreciate. > I will summarize them and send to CCL. > > > Thanks in advance >--------------------------------------------------- > Telkuni Tsuru telkuni:_:venus.dti.ne.jp>To send e-mail to subscribers of CCL put the string CCL: on your Subject: >line> >Send your subscription/unsubscription requests to: >CHEMISTRY-REQUEST:_:ccl.net> > > From owner-chemistry@ccl.net Mon Sep 19 14:32:10 2005 From: "CCL" To: CCL Subject: CCL: delta-scf and TDDFT Message-Id: <-29231-050919095934-22738-QGHIdpNUSNZDeeFZtSXcUw##server.ccl.net> X-Original-From: "Ding Xunlei" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Mon, 19 Sep 2005 21:59:52 +0800 Mime-Version: 1.0 Sent to CCL by: "Ding Xunlei" [dxl##ustc.edu.cn] --Replace strange characters with the "at" sign to recover email address--. Dear chemistry, http://www.scm.com/adflist/0294.html There is a discussion about the delta-scf and TDDFT. According to it, I think that the excited energy of the singlets obtained by TDDFT need not correction using the formula: E (singulet) = 2 E (s+t) - E (triplet). Am I right? Can anybody give a a little more explanation?¡¡¡¡ Yours sincerely, Ding Xunlei 2005-09-19 ______________________________________________ From owner-chemistry@ccl.net Mon Sep 19 15:04:21 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29235-050919150347-3737-8ZOlMZqGwssFfsd6IptP8w!A!server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Mon, 19 Sep 2005 14:03:36 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci!A!UTMB.EDU] --Replace strange characters with the "at" sign to recover email address--. >> A simple solution for publishers would be to ask for >> mandatory deposition of such data as supplementary materials. >1. If publishers hold the data, would we not have to check > with each publisher in turn to get the information? > And if so, how much would it cost? A search engine, such as Google Scholar, should be able to find these data. Many publishers already offer free access to supplementary materials, such as American Chemical Society; many QSAR datasets (including chemical structures) are deposited as supplementary materials to the ACS journal Journal of Chemical Information and Modeling. Of course, the chemical community (editors, reviewers, authors) should ask for open access to computational data, because otherwise the Publishers will not do it. >2. We are, err, blessed with a wide range of file formats, > many of which aren't described, or even readable. > Whose formats would be supported, and would the vendors > and other authors provide the necessary conversion routines? A good starting point is CML - Chemical Markup Language (http://www.xml-cml.org/). See a recent paper on large-scale calculations (250000 compounds from the NCI database), which is a nice application of CML and the new InChi chemical code: A global resource for computational chemistry Peter Murray-Rust1, Henry S. Rzepa2 , James J. P. Stewart3 and Yong Zhang1 Journal of Molecular Modeling (in press) Regards, Ovidiu #################################### Dr. Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0857 USA From owner-chemistry@ccl.net Mon Sep 19 15:49:17 2005 From: "CCL" To: CCL Subject: CCL: Cleaning up dusty deck fortran and converting to C/C++ Message-Id: <-29236-050919153943-21014-QUMMMr75MM7wzm02Pim1ig[#]server.ccl.net> X-Original-From: Andrew Fant Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 19 Sep 2005 14:30:53 -0400 MIME-Version: 1.0 Sent to CCL by: Andrew Fant [fant[#]pobox.com] --Replace strange characters with the "at" sign to recover email address--. CCL wrote: > > Sent to CCL by: John McKelvey [jmmckel%a%attglobal.net] > > --Replace strange characters with the "at" sign to recover email address--. > > Hello! > > I have some old fortran I would like to convert to C.. Have used F2C on > an example code, which had me go back and clean up the fortran first.. > not a bad thing. > > Are there any utilities that would take a dusty fortran deck and clean > it up on its own... i.e. remove unused variables, and the like, for > example? I have a 40,000 line F77 code I would like also to run in C. > > Many thanks, > > John McKelvey John, The usual suspects for cleaning up old Fortran are: Tidy: http://www.unb.ca/fredericton/science/chem/ajit/f_tidy.htm Ftnchek: http://www.dsm.fordham.edu/~ftnchek/ and Flow/Floppy: http://www.netlib.org/floppy/contents.html As far as specific dead code and dead variable detection, most modern Fortran compilers have that capacity built into the optimizer. With regards to optimization, you do realize that moving to C or C++ will probably make your code less optimized and less optimizable, as well, I am sure. And f2c certainly doesn't make for particularly idiomatic c either, as I recall. If the issue is not having access to a good Fortran compiler, you might want to take a look at the intel website. They make available their compilers for certain non-commercial uses. http://www.fortran.com is another good source for such things (disclaimer: I know the people who run the company and may hit them up for a beer at supercomputing if they get a surge in sales from my shameless plug 8-). Hope this helps, Andy From owner-chemistry@ccl.net Mon Sep 19 16:33:53 2005 From: "CCL" To: CCL Subject: CCL: Cleaning up dusty deck fortran and converting to C/C++ Message-Id: <-29237-050919161020-6181-7ybO2v8PY+5DtRaY50pQDQ^^^server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 19 Sep 2005 15:53:03 -0400 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable^^^pollux.cber.nih.gov] --Replace strange characters with the "at" sign to recover email address--. You may wish to look at ftnchek, see URL http://www.dsm.fordham.edu/~ftnchek > From the README-- Ftnchek (short for Fortran checker) is designed to detect certain errors in a Fortran program that a compiler usually does not. Ftnchek is not primarily intended to detect syntax errors. Its purpose is to assist the user in finding semantic errors. Semantic errors are legal in the Fortran language but are wasteful or may cause incorrect operation. For example, variables which are never used may indicate some omission in the program; uninitialized variables contain garbage which may cause incorrect results to be calculated; and variables which are not declared may not have the intended type. ------ The NETLIB repository has a couple programs named floppy and flow that analyze Fortran source code, see URL http://www.netlib.org/floppy/ ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable AT nih*gov ALT email: rvenable AT speakeasy*org ------------------------------------- www.redcross.org On Mon, 19 Sep 2005, CCL wrote: > Sent to CCL by: John McKelvey [jmmckel%a%attglobal.net] > I have some old fortran I would like to convert to C.. Have used F2C > on an example code, which had me go back and clean up the fortran > first.. not a bad thing. > > Are there any utilities that would take a dusty fortran deck and clean > it up on its own... i.e. remove unused variables, and the like, for > example? I have a 40,000 line F77 code I would like also to run in C. From owner-chemistry@ccl.net Mon Sep 19 22:10:36 2005 From: "CCL" To: CCL Subject: CCL: Cleaning up dusty deck fortran and converting to C/C++ Message-Id: <-29238-050919220534-3305-rp07L/TcICkK9EsQlZlfRQ++server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 19 Sep 2005 21:03:39 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel++attglobal.net] --Replace strange characters with the "at" sign to recover email address--. Andy, Thanks for the suggestions. The issue is that I am collaborating with someone who has his code in C++ and mine is in fortran. He wants it all in C++, so as I am not at all fluent in C of C++ I have taken alternate routes. I have used both tidy and ftnchek to spot dead code; f2c does a good job also. Many thanks, John CCL wrote: >Sent to CCL by: Andrew Fant [fant[#]pobox.com] > >--Replace strange characters with the "at" sign to recover email address--. > >CCL wrote: > > >>Sent to CCL by: John McKelvey [jmmckel%a%attglobal.net] >> >>--Replace strange characters with the "at" sign to recover email address--. >> >>Hello! >> >>I have some old fortran I would like to convert to C.. Have used F2C on >>an example code, which had me go back and clean up the fortran first.. >>not a bad thing. >> >>Are there any utilities that would take a dusty fortran deck and clean >>it up on its own... i.e. remove unused variables, and the like, for >>example? I have a 40,000 line F77 code I would like also to run in C. >> >>Many thanks, >> >>John McKelvey >> >> > >John, > The usual suspects for cleaning up old Fortran are: > >Tidy: http://www.unb.ca/fredericton/science/chem/ajit/f_tidy.htm > >Ftnchek: http://www.dsm.fordham.edu/~ftnchek/ > >and > >Flow/Floppy: http://www.netlib.org/floppy/contents.html > >As far as specific dead code and dead variable detection, most modern Fortran >compilers have that capacity built into the optimizer. > >With regards to optimization, you do realize that moving to C or C++ will >probably make your code less optimized and less optimizable, as well, I am sure. > And f2c certainly doesn't make for particularly idiomatic c either, as I >recall. If the issue is not having access to a good Fortran compiler, you might >want to take a look at the intel website. They make available their compilers >for certain non-commercial uses. http://www.fortran.com is another good source >for such things (disclaimer: I know the people who run the company and may hit >them up for a beer at supercomputing if they get a surge in sales from my >shameless plug 8-). > >Hope this helps, > Andy> > > > > > > From owner-chemistry@ccl.net Mon Sep 19 22:41:42 2005 From: "CCL" To: CCL Subject: CCL: Cleaning up dusty deck fortran and converting to C/C++ Message-Id: <-29239-050919181624-14457-t/j/+87T0b7JhlJalKwNfg]-[server.ccl.net> X-Original-From: Daniel Macks Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 19 Sep 2005 17:32:11 -0400 Mime-Version: 1.0 Sent to CCL by: Daniel Macks [dmacks]-[netspace.org] --Replace strange characters with the "at" sign to recover email address--. > > Are there any utilities that would take a dusty fortran deck and clean > it up on its own... i.e. remove unused variables, and the like, for > example? I have a 40,000 line F77 code I would like also to run in C. There are lots of stand-alone "lint"-type programs that could help, both before and after f2c conversion, and many compilers have flags that are useful as well. A quick google for [fortran lint] gave several useful-sounding utilities for the fortran side of things. After conversion to C, there's the usual "lint", and gcc has family of -Wunused* and other flags that can help (do these also work in the for gcc-derived fortran compilers?). dan -- Daniel Macks dmacks]-[netspace.org http://www.netspace.org/~dmacks