From owner-chemistry@ccl.net Wed Mar 4 04:04:01 2009 From: "Marcel Swart marcel.swart__icrea.es" To: CCL Subject: CCL: van der Waals parameter for iron Message-Id: <-38739-090304035700-10432-phqL67u6Z5Jz/Q2lhyscVQ..server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 4 Mar 2009 08:50:21 +0100 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart:-:icrea.es] The most troublesome part of force field development for metal-complexes is getting the bonded parameters; for the van der Waals parameters you could use either the values that I borrowed from the MM2 force field, (see below), or the value that is used for the heme group in the contributed parameter sets within Amber (see: http://www.pharmacy.manchester.ac.uk/bryce/amber). atom(s) Emin Rmin gamma NOTES =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D OW 0.1520 3.5366 12.00 TIP3P water model FE 0.0500 2.4000 12.00 Heme parameter file FE 0.35325 4.3800 12.00 MM2 parameters (M. Swart added) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Note that the Rmin value given here is double what other programs expect, so for instance for use within Amber it should be divided by 2. Note also the paper in J. Comput. Chem. with the title "New AMBER Force Field Parameters of Heme Iron for Cytochrome P450s Determined by Quantum Chemical Calculations of Simpli?ed Models" J Comput Chem 26: 818 ? 826, 2005 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart ~~ icrea.es marcel.swart ~~ udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-chemistry@ccl.net Wed Mar 4 05:22:01 2009 From: "xunlei ding dingxunlei:_:gmail.com" To: CCL Subject: CCL:G: G- How to retain the symmetry in a SCF calculation ? Message-Id: <-38740-090304051240-12224-48I3mMBZGFFlBr2hE6JfTA*server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Date: Wed, 4 Mar 2009 18:12:23 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei|gmail.com] Dear Johannes, Sometimes scf=3DQC works but not always. I hope there be a better way for this problem. It seems that we can use IOP, as is described as: IOp(5/15) Apply Abelian symmetry constraints on orbitals. 0 Default (1 for L502, 2 for L501 and L506). 1 No. 2 Yes, keep occupation of each irrep the same as the initial guess. 3 Yes, keep overall wavefunction the same as the initial guess, but doing the minimal amount of orbital switching to accomplish this. 00 Default (use Abelian symmetry in diagonalization). 10 Use Abelian symmetry in diagonalization. 20 Do not use Abelian symmetry in diagonalization. But in my test, iop(5/15=3D2) doesn't work. Any more suggestions? Thanks a lot! Best regards, Ding 2009/2/13 Johannes Hachmann jh388[*]cornell.edu : > > Sent to CCL by: "Johannes Hachmann" [jh388!A!cornell.edu] > Hi Ding, > > use SCF=3DQC (however quadratically convergent SCF is a bit costy...). Se= e > description under http://www.gaussian.com/g_ur/k_guess.htm on the bottom > together with GUESS=3DALTER. This is not a particularly elegant way to do > things (compared to just specifying the state symmetry in e.g. MOLPRO) bu= t > it works. You might want to use the STABLE option so that you know whethe= r > you have instabilities to which other states and which additional MO swap= s > you might want to perform. > > Best > > Johannes > > --------------------------------------------------------------- > Johannes Hachmann > (Dipl.-Chem., M.Sc.) > > Chan Research Group > 140D Baker Laboratory > Department of Chemistry and Chemical Biology > Cornell University > Ithaca, NY 14853-1301 > USA > --------------------------------------------------------------- >> -----Original Message----- >> From: owner-chemistry+jh388=3D=3Dcornell.edu[]ccl.net >> [mailto:owner-chemistry+jh388=3D=3Dcornell.edu[]ccl.net] On Behalf >> Of xunlei ding dingxunlei::gmail.com >> Sent: Friday, February 13, 2009 3:42 AM >> To: Hachmann, Johannes >> Subject: CCL:G: G- How to retain the symmetry in a SCF calculation ? >> >> >> Sent to CCL by: xunlei ding [dingxunlei.:.gmail.com] Dear CCLers, >> >> In the manual of G03, the key word "SCF=3D Symm" is discribed as below: >> Retain all symmetry constraints: make the number of occupied >> orbitals of each symmetry type (abelian irreducible >> representation) match that of the initial guess. Use this >> option to retain a specific state of the wavefunction >> throughout the calculation. It is the default only for GVB >> calculations. >> >> But sometimes it doesn't work and the last state is different >> from the initial state. >> >> Could you give me more suggestions on how to retain the >> symmetry in a SCF calculation? >> >> Thanks! >> >> Best regards, >> Ding >> >> >> >> -=3D This is automatically added to each message by the mailing >> script =3D- To recover the email address of the author of the >> message, please change the strange characters on the top line >> to the [] sign. You can also look up the X-Original-From: line >> in the mail header.> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search)> >> > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: search)> > > --=20 ------------------------------------------------------ Xun-Lei Ding Associate Research Professor of Physical Chemistry State Key Lab for Struct. Chem. of Unstable and Stable Species Institute of Chemistry, The Chinese Academy of Sciences Zhongguancun North First Street 2=A3=AC Beijing 100190, P. R. China Phone 86-10-62568330 Fax 86-10-62559373 From owner-chemistry@ccl.net Wed Mar 4 08:45:00 2009 From: "Taner Atalar taneratalar#,#gmail.com" To: CCL Subject: CCL:G: recommendations for computer hardware in windows Message-Id: <-38741-090304074854-3572-/lDrst3lzlxiFqAbi187MQ!^!server.ccl.net> X-Original-From: "Taner Atalar" Date: Wed, 4 Mar 2009 07:48:51 -0500 Sent to CCL by: "Taner Atalar" [taneratalar(-)gmail.com] I plan to buy a PC for moderate size organic compounds' calculations at DFT level. I plan to use Gaussian 03W and/or Spartan for this purpose. So I need a computer hardware recommendations. Thanks for help. Taner From owner-chemistry@ccl.net Wed Mar 4 09:19:01 2009 From: "mi yang miyang3790%a%gmail.com" To: CCL Subject: CCL:G: Excited state dipole moment with DFT Message-Id: <-38742-090304084856-24664-8ioe+jfcGJnTQQtXcplU3w#server.ccl.net> X-Original-From: "mi yang" Date: Wed, 4 Mar 2009 08:48:52 -0500 Sent to CCL by: "mi yang" [miyang3790]^[gmail.com] Hi CCl users! Is it possible in G03 to calculate/estimate the excited dipole moment at DFT method by applying some finite field like as in ADF or some other way..? if someone answer I would be thankful to him/her. Miyang From owner-chemistry@ccl.net Wed Mar 4 09:59:00 2009 From: "Justin Finnerty justin.finnerty~~uni-oldenburg.de" To: CCL Subject: CCL:G: IRC calculation Message-Id: <-38743-090304090419-333-X5hokb3Sgxed6lFJMFK9nA:server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 04 Mar 2009 14:12:36 +0100 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty*_*uni-oldenburg.de] On Tue, 2009-03-03 at 09:48 -0500, Kavitha Velappan kavitha.velappan(a)gmail.com wrote: > Sent to CCL by: "Kavitha Velappan" [kavitha.velappan_-_gmail.com] > Hi all, > > I tried to do IRC calculation to follow the reaction path for conformer interconversion (Dimethoxymethane G+G- to G-G- conformer - rotation around OCH3 bond). The route section looks like this: > > #N RB3LYP/6-31++G** IRC=(CalcFC,maxpoints=12) I have had this issue whenever I do an IRC with DFT in gaussian. The problems are as you see, the IRC only goes in one direction and doesn't reach maxpoints. I found that the best solution to this is to reduce the STEPSIZE. The default is 10 and I have had much success with STEPSIZE=4 or 3. (You have to increase MAXPOINTS accordingly!) Using this I have successfully used IRC to go from the TS to close to the ground state. Using a small stepsize will increase the length of the calculation but not as much as it first appears because the previous step of the IRC is now much closer to the new step so each step converges in two or three cycles. The other issue is getting both the forward and reverse directions to work. I have found no reliable way to do this automatically in gaussian using DFT - gaussian always seems to go in one direction! My normal solution is to manually modify the TS structure in the direction gaussian didn't go and start the IRC from the modified structure. How I modify the structure is of course based on the motion vectors of the imaginary frequency. PS Your input uses CALCFC, surely you could use READFC from the freq calculation for the TS? Cheers Justin -- Dr Justin Finnerty Rm W3-1-165 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Wed Mar 4 10:29:00 2009 From: "Pierre Archirel pierre.archirel(a)lcp.u-psud.fr" To: CCL Subject: CCL:G: Printing of J and K Message-Id: <-38744-090304082007-20786-+4gZDyeX03a93fLVFd5IAQ=-=server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 04 Mar 2009 13:30:59 +0100 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel]_[lcp.u-psud.fr] Dear collegues, Is there some simple way for having simply Jij and Kij integrals between molecular orbitals, printed by usual codes like Gaussian 03 or Gamess US? Note that: 1- I have large basis sets: 1200 cgto's 2- I need Jij and Kij for a little number only (say 10) of virtual orbitals of the HF procedure Thanks a lot in advance, PS I have checked that in Gamess NPRINT=4 yields integrals between cgto's only Pierre Archirel, LCP, Universite Paris-Sud, Orsay, France __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel(0)lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Wed Mar 4 11:04:00 2009 From: "John McKelvey jmmckel*_*gmail.com" To: CCL Subject: CCL:G: Excited state dipole moment with DFT Message-Id: <-38745-090304103352-15274-96aC9UJd8ghI8rSrMVBfjg[]server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=000e0cd28d78b4f54904644cc6f6 Date: Wed, 4 Mar 2009 10:33:40 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel-#-gmail.com] --000e0cd28d78b4f54904644cc6f6 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit I think that the ES density is ultimately required to compute ES gradients. It might be possible that G03 provides the ES dipole given the ES density. John McKelvey On Wed, Mar 4, 2009 at 8:48 AM, mi yang miyang3790%a%gmail.com < owner-chemistry++ccl.net> wrote: > > Sent to CCL by: "mi yang" [miyang3790]^[gmail.com] > Hi CCl users! > > Is it possible in G03 to calculate/estimate the excited dipole moment at > DFT method by applying some finite field like as in ADF or some other way..? > if someone answer I would be thankful to him/her. > > Miyang> > > --000e0cd28d78b4f54904644cc6f6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I think that the ES density is ultimately required to compute ES gradients.= =A0 It might be possible that G03 provides the ES dipole given the ES densi= ty.

John McKelvey

On Wed, Mar 4, 2= 009 at 8:48 AM, mi yang miyang3790%a%gmail.com= <owner= -chemistry++ccl.net> wrote:

Sent to CCL by: "mi =A0yang" [miyang3790]^[gmail.com]
Hi CCl users!

Is it possible in G03 to calculate/estimate the excited dipole moment at DF= T method by applying some finite field like as in ADF or some other way..?<= br> if someone answer I would be thankful to him/her.

Miyang



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--000e0cd28d78b4f54904644cc6f6-- From owner-chemistry@ccl.net Wed Mar 4 14:57:00 2009 From: "Rajarshi Guha rguha a indiana.edu" To: CCL Subject: CCL: Call for CINF Symposia Proposals Message-Id: <-38746-090304145255-14142-OmW3bCUamkvS2Pm5JOKwkA.:.server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Wed, 4 Mar 2009 14:01:30 -0500 Mime-Version: 1.0 (Apple Message framework v930.3) Sent to CCL by: Rajarshi Guha [rguha,indiana.edu] As part of expanding the programming in the CINF division, we would like to solicit symposia proposals for future ACS meetings. Given the diversity of the division, we are interested in a wide variety of topics ranging from * Various aspects of cheminformatics research including algorithm development and applications in various areas * Cross-disciplinary topics such as those at the intersection of cheminformatics and bioinformatics * Advances in chemical information managment, access, dissemination and communication * Research and applications in the area of chemical databases * New technologies that enhance and advance the use of chemical information * Intellectual property issues that might address open source/data/ access * Instruction For examples of recent symposia topics visit the following links: http://oasys.acs.org/acs/237nm/techprogram/CINF.HTM http://oasys.acs.org/acs/236nm/techprogram/CINF.HTM http://oasys.acs.org/acs/235nm/techprogram/CINF.HTM http://oasys.acs.org/acs/234nm/techprogram/CINF.HTM but of course, if you have ideas not covered there we'd be happy to consider them. We are currently interested in proposals for the San Francisco (Spring 2010) and Boston (Fall 2010) meetings, but will also consider symposia proposals for future meetings. We should point out that due to programming constraints and recurring sessions, we can't include all proposed sessions in a given meeting. However we hope that prospective session organizers will consider organizing inlater meetings. As a session organizer, you'd specify the topic of the session, seekout speakers (either by invitation or by putting out a call for papers) and arrange the talks in the session. If you're new to ACS programming, you'll be paired with an experienced CINF member to helpout with the details of setting up the session. If you're interested in organizing a symposia, please send an email to Rajarshi Guha (rajarshi.guha_-_gmail.com) with the title of the session and a brief description of the topic and scope. If the proposal is approved by the CINF program committee, you'll be included in the schedule for the appropriate meeting and you can then start organizing! If you have any questions feel free to contact me at rajarshi.guha_-_gmail.com or by phone at 814 404 5449 PS. If you happen to be attending the Spring ACS in Salt Lake City, the Program Committee will be meeting from 9am to 12pm on Saturday 21st March. If you are interested in getting involved in programming, I encourage you to drop by. ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Q: What's polite and works for the phone company? A: A deferential operator. From owner-chemistry@ccl.net Wed Mar 4 17:46:01 2009 From: "Roger Kevin Robinson scu98rkr#,#gmail.com" To: CCL Subject: CCL:G: CCL : Calculating Reaction Rates involving metals surfaces using Polyrate Message-Id: <-38747-090304121444-482-lbfEz6gawauIZ6g78jPxAA##server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 04 Mar 2009 16:56:33 +0000 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [scu98rkr{:}gmail.com] Hi, I have been using looking at reactions in the gas phase using Gaussian. Then using polyrate and some RRKM codes to calculate High Pressure rate data. We are now interested in looking reactions on metal surfaces. I dont have much experience with looking at surfaces although I have posted on here before and people have advised me to look at SIESTA and I went on a 1 week course last year so I know have some experience with this software. However I still want to calculate rate data I was previous using the GAUSSRATE interface I notice POLYRATE has some other interfaces. GAMESSPLUSRATE GAUSSRATE JAGUARATE MC-TINKERATE MORATE MULTILEVELRATE Would any of these codes be good for looking at surfaces and do you think I'd be able to link them to POLYRATE to calculate reaction rates involving surfaces ? Any help appreciated Thanks Roger -- Dr. R.Robinson Research Associate Department of Mechanical Engineering Imperial College London - South Kensington Campus London SW7 2AZ UK Tel: +44 20 7589 5111 Ext.57112 Email: r.robinson]^[imperial.ac.uk From owner-chemistry@ccl.net Wed Mar 4 18:21:01 2009 From: "Sriraj Srinivasan ss537%a%drexel.edu" To: CCL Subject: CCL:G: IRC calculation Message-Id: <-38748-090304123043-2260-GgQGGE73fv3xAgOALoDHjA^-^server.ccl.net> X-Original-From: Sriraj Srinivasan Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 04 Mar 2009 11:40:08 -0500 MIME-Version: 1.0 Sent to CCL by: Sriraj Srinivasan [ss537:_:drexel.edu] Hi Kavitha=2C Make sure that your hessian is correct enough to go in both directions=2E= This is critical for an IRC calculation to succeed=2E I do DFT calculati= ons and have found no problems as such=2E Sriraj ----- Original Message ----- > From=3A =22Justin Finnerty justin=2Efinnerty=7E=7Euni-oldenburg=2Ede=22 =3C= owner-chemistry=40ccl=2Enet=3E Date=3A Wednesday=2C March 4=2C 2009 8=3A12 am Subject=3A CCL=3AG=3A IRC calculation =3E = =3E Sent to CCL by=3A Justin Finnerty =5Bjustin=2Efinnerty*=5F*uni-oldenb= urg=2Ede=5D =3E = =3E On Tue=2C 2009-03-03 at 09=3A48 -0500=2C Kavitha Velappan =3E kavitha=2Evelappan(a)gmail=2Ecom wrote=3A =3E =3E Sent to CCL by=3A =22Kavitha Velappan=22 =5Bkavitha=2Evelappan=5F= -=5Fgmail=2Ecom=5D =3E =3E Hi all=2C =3E =3E = =3E =3E I tried to do IRC calculation to follow the reaction path for = =3E conformer interconversion (Dimethoxymethane G+G- to G-G- conformer = =3E - rotation around OCH3 bond)=2E The route section looks like this=3A =3E =3E = =3E =3E =23N RB3LYP/6-31++G** IRC=3D(CalcFC=2Cmaxpoints=3D12) =3E = =3E I have had this issue whenever I do an IRC with DFT in gaussian=2E T= he =3E problems are as you see=2C the IRC only goes in one direction and = =3E doesn=27treach maxpoints=2E =3E = =3E I found that the best solution to this is to reduce the STEPSIZE=2E T= he =3E default is 10 and I have had much success with STEPSIZE=3D4 or 3=2E = (You =3E have to increase MAXPOINTS accordingly!) Using this I have = =3E successfullyused IRC to go from the TS to close to the ground = =3E state=2E Using a small =3E stepsize will increase the length of the calculation but not as = =3E much as =3E it first appears because the previous step of the IRC is now much = =3E closerto the new step so each step converges in two or three cycles=2E= =3E = =3E The other issue is getting both the forward and reverse directions to= =3E work=2E I have found no reliable way to do this automatically in = =3E gaussianusing DFT - gaussian always seems to go in one direction! = =3E My normal =3E solution is to manually modify the TS structure in the direction =3E gaussian didn=27t go and start the IRC from the modified structure=2E= = =3E How I =3E modify the structure is of course based on the motion vectors of the =3E imaginary frequency=2E =3E = =3E PS Your input uses CALCFC=2C surely you could use READFC from the fre= q =3E calculation for the TS=3F =3E = =3E Cheers =3E Justin =3E = =3E -- = =3E Dr Justin Finnerty =3E Rm W3-1-165 Ph 49 (441) 798 3726 =3E Carl von Ossietzky Universit=E4t Oldenburg =3E = =3E = =3E = =3E -=3D This is automatically added to each message by the mailing = =3E script =3D- =3E To recover the email address of the author of the message=2C please = =3E changethe strange characters on the top line to the =40 sign=2E You = =3E can also =3E look up the X-Original-From=3A line in the mail header=2E =3E = =3E E-mail to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A =3E http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage =3E = =3E E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or use =3E http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage =3E = =3E Subscribe/Unsubscribe=3A = =3E http=3A//www=2Eccl=2Enet/chemistry/sub=5Funsub=2Eshtml =3E = =3E Before posting=2C check wait time at=3A http=3A//www=2Eccl=2Enet =3E = =3E Job=3A http=3A//www=2Eccl=2Enet/jobs = =3E Conferences=3A = =3E http=3A//server=2Eccl=2Enet/chemistry/announcements/conferences/ =3E Search Messages=3A http=3A//www=2Eccl=2Enet/chemistry/searchccl/index= =2Eshtml =3E = =3E If your mail bounces from CCL with 5=2E7=2E1 error=2C check=3A =3E http=3A//www=2Eccl=2Enet/spammers=2Etxt =3E = =3E RTFI=3A http=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/ =3E = =3E = =3E From owner-chemistry@ccl.net Wed Mar 4 20:37:01 2009 From: "Anandarup Goswami ananda1911[A]gmail.com" To: CCL Subject: CCL: Rotating a structure during the presentation in powerpoint in mac Message-Id: <-38749-090304185437-17274-Uzea3R6gWJ8FYynUGAws5Q[#]server.ccl.net> X-Original-From: Anandarup Goswami Content-Type: multipart/alternative; boundary=001517573dd08ba2be046453c5ed Date: Wed, 4 Mar 2009 18:54:26 -0500 MIME-Version: 1.0 Sent to CCL by: Anandarup Goswami [ananda1911*gmail.com] --001517573dd08ba2be046453c5ed Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all, I am using powewrpoint in my mac to make presentation. I have to put some calculated structures in my slides. I have been using chemcraft and gaussview to make the picture. But it would have been much better if I could allow some of my structures to rotate freely (like a movie file) during my presentation. I am relatively new to this field and have no experience in this kind of 3D effect particularly in mac. Any help regarding this would be highly appreciated. Thanks, Anandarup Goswami --001517573dd08ba2be046453c5ed Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all,
I am using powewrpoint in my mac to make presentation. I have to= put some calculated structures in my slides. I have been using chemcraft a= nd gaussview to make the picture. But it would have been much better if I c= ould allow some of my structures to rotate freely (like a movie file) durin= g my presentation. I am relatively new to this field and have no experience= in this kind of 3D effect particularly in mac. Any help regarding this wou= ld be highly appreciated.
Thanks,
Anandarup Goswami
--001517573dd08ba2be046453c5ed-- From owner-chemistry@ccl.net Wed Mar 4 21:33:01 2009 From: "David Mannock dmannock(!)ualberta.ca" To: CCL Subject: CCL:G: recommendations for computer hardware in windows Message-Id: <-38750-090304184018-8274-PSdynCfptnDCkWeF/srY3A(-)server.ccl.net> X-Original-From: David Mannock Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Wed, 04 Mar 2009 16:39:47 -0700 Mime-Version: 1.0 Sent to CCL by: David Mannock [dmannock(_)ualberta.ca] Taner, I just purchased system components from=20 Newegg.ca and Superbiiz.com. I had thought of=20 buying an AMD Phenom II system locally ($700CDN)=20 with lots (8GB) of memory running under Vista 64=20 bit OS, but there is not much room for upgrades=20 with that platform unless you buy a DDR3 mobo and=20 memory (+$500 =3D$1200CDN) and Intel's new iC7=20 chips are faster, but all the components are very=20 expensive, so an entry level system is $1500.=20 After much searching I found a Tyan S2912-E board=20 on sale at Newegg for $90 CDN) and 2 quad-core=20 third generation socket F chips for $170US each=20 at Superbiiz.com. As you can see from the totals=20 below, I have a system which costs about $1100=20 CDN with 2 x Opteron socket F 3rd gen processors,=20 2 x 500GB HDs, 8GB DDR2 DRAM, an ATI 3700=20 workstation video card and wireless PCI adapter.=20 I will buy a KVM switch and use the monitor,=20 keyboard and mouse from my desktop which has a=20 good UPS back up. The new system will run Vista=20 64 ($75 CDN, Univ of Alberta price), VMware=20 (free) and Deep Freeze enterprise edition ($13)=20 http://www.faronics.com/html/deepfreeze.asp. Here is my Newegg.ca order: 1 TYAN S2912G2NR Dual 1207(F) NVIDIA nForce=20 Professional 3600 Extended ATX Server Motherboard - Retail Item #: N82E16813151070 $87.49 Subtotal $87.49 Handling $4.44 UPS INTL CAN Standard (GND) $1.25 Order Total $93.18 CAN $ Qty Product Description Price Shipped from CA, USA 2 Seagate ST3640323AS 640GB 7200 RPM SATA 3.0Gb/s Hard Drive - OEM Item #: N82E16822148335 $159.98 CDN ($79.99 ea) 1 TP-LINK TL-WN651G 32bit PCI G & eXtended=20 Range 108M Wireless Adapter - Retail Item #: N82E16833704006 $27.49 1 ATI 100-505564 FirePro V3700 256MB PCI=20 Express 2.0 x16 Workstation Video Card - OEM Item #: N82E16814195073 $106.49 CDN 1 hec X-Power Pro 650 650W Continuous -.- 40=B0C=20 ATX12V / EPS12V SLI Ready CrossFire Ready Power Supply - Retail Item #: N82E16817339024 $49.99 CDN Shipped from NJ, USA 8 Kingston 1GB 240-Pin DDR2 SDRAM DDR2 667=20 (PC2 5300) ECC Unbuffered Intel Certified Server=20 Memory Model KVR667D2E5/1GI - Retail Item #: N82E16820134333 $119.92 CDN ($14.99 ea) 1 HEC 69R5BB Black Steel ATX Full Tower Computer Case - Retail Item #: N82E16811121018 $58.74 CDN Subtotal $522.61 Handling $26.13 UPS INTL CAN Standard (GND) $63.55 Order Total $612.29 CAN$ I used a purchase order to buy 2 AMD Opteron=20 quad-core 2376 2.3 MHz processors=20 http://products.amd.com/en-us/OpteronCPUDetail.aspx?id=3D489&f1=3DThird-Gene= ration+AMD+Opteron%99&f2=3D&f3=3D&f4=3D512&f5=3D&f6=3D&f7=3D&f8=3D&f9=3D&f10= =3D4& for $170 USD each + $60 shipping. I purchased 2 new Dynatron A5MG's from an ebay=20 seller for $20US each here. These are 4.1" sq for=20 the 3rd generation Opteron chips. http://stores.ebay.ca/UrCooler The new AMD price list for these chips is on=20 their web site, but you have to buy through a=20 reseller. Contact Michelle Ousy=20 (michelle-.-ewiz.com) at Superbiiz for processor=20 availability. Tigerdirect also has these but for=20 an extra $30 each. Also check out Starmicro. Make=20 sure you are getting a new cpu. Some are OEM, not=20 boxed. A few may be tested pulls. Check this first! AMD reviews of servers with opteron chips=20 http://www.amd.com/us-en/Processors/ProductInformation/0,,30_118_8825_15885,= 00.html Notice the price difference vs Dell!! The benefits of this system are the dual=20 processors, lower power consumption (& thus heat)=20 for the cpus vs Phenom II chips. The Phenom II=20 chips cannot be used on a 2 cpu board and from=20 what I have read cannot be used in this config=20 for technical reasons. These socket F (1207)=20 boards will support the new 6 core processors due=20 in late 2009, so there is a processor upgrade=20 possible although with this board, the DDR2=20 667MHz DRAM will not change, you can expand the=20 RAM up to 64GB full capacity. Basic graphics on=20 board, but workstation video card is better=20 http://ati.amd.com/products/firepro/index.html.=20 It is a new design openGL card. Lots of room for=20 memory if you can afford it. I started at 8GB as=20 it was a reasonable price. I can wait for the=20 chips to come down in price. The 2 HDs mean that=20 in principle, you could have one HD for Vista64 and the other for LINUX. The down side. The mobo bios needs upgrading.=20 This can be done through Tyan for $20 or you can=20 get your tech department to do this via a CD or a=20 USB memory stick details at Tyan. The mobo=20 designation S2912 and S2912-E are not the same=20 (specs are at Tyan). Only the -E model will=20 support QC processors. The reviews at Newegg say=20 that this is the -E version as many people have=20 done the bios upgrade to support third generation=20 processors. There is some speculation about=20 whether you need a dual core or a quad core=20 processor to do this. A new cheap DC processor is=20 under $100, but Tyan will do this for you in the=20 USA. You need to upgrade to bios v4.=20 Alternatively you can get a replacement bio chip=20 > from Biosman. There was one problem noted at that=20 site for the S2912 mobo which was a question=20 about shutting off the on board graphics when=20 using a graphics card. That may require a bios=20 chip modification. Prices are $27 . The choice of computer case is important. Most=20 ATX cases built for gaming have enough fans to=20 cool everything, but these mobos are extended=20 (E-ATX) forms at 12"x13" , so you need to get a=20 box 22x8x20". The Hec case is ideal and is well=20 built and CHEAP. It must accommodate the cpu fans=20 which are 2U (double height). I have tried to=20 pick components, like the cpus, PS, etc which put=20 out less heat, but fast HDs produce more heat.=20 The Seagates were a compromise between ultrafast=20 drives and intelligent drives by Western Digital whose speed varies with= load. OK, well there is my input. All of the items will=20 be here in a week and my tech services shop will=20 do the assembly and software installation for me.=20 This should give me a decent desktop workstation=20 for $1100-1200CDN. Check here for cpu benchmarks=20 and go up one dir to see others.=20 http://www.cpubenchmark.net/high_end_cpus.html=20 This set up (the dual cpu Opteron 2354 processor=20 info is provided) should be up there with the new=20 Intel i7 processors, but have a lot of upgrade=20 potential in the future as prices come down. AMD=20 tends to incorporate this upgrade philosophy into=20 their designs, Intel do not! Last of all, with=20 Sun, SGI and Dell asking $10k+ for one of these=20 you are getting a very good deal. If you can=20 afford a newer mobo spend the extra $300 now.=20 Incidentally, these processors are numbered as=20 follows: 2 or 8 =3D no of processors per mobo. 1,2,=20 or 3 =3D generation of processor. I think you may=20 be able to use 8000 series chips on 2000 series=20 boards, but not the other way around, but I am=20 not sure about this. Also the lowest priced 4 cpu=20 board I found was a Tyan board at ~$350US, but=20 the 8000 series chips cost too much for me. My=20 department tech guy is very interested in this=20 little project and will help me with set up, as=20 there is the potential here to help=20 crystallographers and NMR spectroscopy people in=20 our department and put together a multi-cpu QC=20 workstation farm for what would be considered to=20 be peanuts. Then again with the recent interest=20 in doing graphics work on multiple Sony PS3 's=20 using Yellow Dog Linux, maybe we are all wasting our time. Dave At 05:48 AM 3/4/2009, you wrote: >Sent to CCL by: "Taner Atalar" [taneratalar(-)gmail.com] >I plan to buy a PC for moderate size organic=20 >compounds' calculations at DFT level. I plan to=20 >use Gaussian 03W and/or Spartan for this purpose. > >So I need a computer hardware recommendations. Thanks for help. > >Taner > > > >-=3D This is automatically added to each message by the mailing script =3D-Dr David Mannock 339 Med Sci Bldg, Dept of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7 Canada Tel: 1-780-492-2412 FAX: 1-780-492-0886=20 From owner-chemistry@ccl.net Wed Mar 4 22:28:01 2009 From: "Igor Filippov Contr igorf=-=helix.nih.gov" To: CCL Subject: CCL: Rotating a structure during the presentation in powerpoint in mac Message-Id: <-38751-090304222547-12034-IJU5tTo3Ph5S+qd0mwNyPw- -server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 04 Mar 2009 22:25:23 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf*o*helix.nih.gov] Jmol is free and works everywhere AFAIK. http://jmol.sourceforge.net/ Don't use powerpoint and the problems will go away :) Igor On Wed, 2009-03-04 at 18:54 -0500, Anandarup Goswami ananda1911[A]gmail.com wrote: > Hi all, > I am using powewrpoint in my mac to make presentation. I have to put > some calculated structures in my slides. I have been using chemcraft > and gaussview to make the picture. But it would have been much better > if I could allow some of my structures to rotate freely (like a movie > file) during my presentation. I am relatively new to this field and > have no experience in this kind of 3D effect particularly in mac. Any > help regarding this would be highly appreciated. > Thanks, > Anandarup Goswami -- Igor Filippov [Contr] From owner-chemistry@ccl.net Wed Mar 4 23:19:01 2009 From: "hirdesh kumar hirdeshs8]|[gmail.com" To: CCL Subject: CCL: Rotating a structure during the presentation in powerpoint in mac Message-Id: <-38752-090304231629-7117-gooNh6Y/y61u4w2TbrRNoQ,+,server.ccl.net> X-Original-From: hirdesh kumar Content-Type: multipart/alternative; boundary=001485ec10183b504b0464576d7b Date: Thu, 5 Mar 2009 09:46:04 +0530 MIME-Version: 1.0 Sent to CCL by: hirdesh kumar [hirdeshs8 ~ gmail.com] --001485ec10183b504b0464576d7b Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Anandarup; I think you should use *emovie plug-in* of pymol. Here is the link: http://www.weizmann.ac.il/ISPC/eMovie_download.html --001485ec10183b504b0464576d7b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Anandarup;
I think you should use emovie plug-in of pymol. Here is the link:
http://www.weizmann.ac.il/ISPC/eMovie_download.html

--001485ec10183b504b0464576d7b-- From owner-chemistry@ccl.net Wed Mar 4 23:53:00 2009 From: "Johannes Hachmann jh388 ~~ cornell.edu" To: CCL Subject: CCL:G: G- How to retain the symmetry in a SCF calculation ? Message-Id: <-38753-090304232022-9722-gpEMuLLI/o6P/wMdxDY/qw*|*server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Date: Wed, 4 Mar 2009 23:19:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh388_._cornell.edu] Hi Ding, sorry, never ran into this problem. Note that you might have to try a = number of orbital swaps to get to the wavefunction irrep you want. Also, = in case you use the STABLE keyword, DO NOT use STABLE=3DOPT because that = will likely bring you back to a more stable wavefunction of different = symmetry.=20 Hope that helps Best Johannes --------------------------------------------------------------- Johannes Hachmann (Dipl.-Chem., M.Sc.) Chan Research Group 140D Baker Laboratory Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853-1301 USA --------------------------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh388=3D=3Dcornell.edu[-]ccl.net=20 > [mailto:owner-chemistry+jh388=3D=3Dcornell.edu[-]ccl.net] On Behalf=20 > Of xunlei ding dingxunlei:_:gmail.com > Sent: Wednesday, March 04, 2009 5:12 AM > To: Hachmann, Johannes > Subject: CCL:G: G- How to retain the symmetry in a SCF calculation ? >=20 >=20 > Sent to CCL by: xunlei ding [dingxunlei|gmail.com] Dear Johannes, >=20 > Sometimes scf=3DQC works but not always. > I hope there be a better way for this problem. >=20 > It seems that we can use IOP, as is described as: >=20 > IOp(5/15) > Apply Abelian symmetry constraints on orbitals. >=20 > 0 Default (1 for L502, 2 for L501 and L506). > 1 No. > 2 Yes, keep occupation of each irrep the same as the=20 > initial guess. > 3 Yes, keep overall wavefunction the same as the initial guess, > but doing the minimal amount > of orbital switching to accomplish this. > 00 Default (use Abelian symmetry in diagonalization). > 10 Use Abelian symmetry in diagonalization. > 20 Do not use Abelian symmetry in diagonalization. >=20 > But in my test, iop(5/15=3D2) doesn't work. >=20 > Any more suggestions? >=20 > Thanks a lot! >=20 > Best regards, > Ding >=20 >=20 >=20 > 2009/2/13 Johannes Hachmann jh388[*]cornell.edu=20 > : > > > > Sent to CCL by: "Johannes Hachmann" [jh388!A!cornell.edu] Hi Ding, > > > > use SCF=3DQC (however quadratically convergent SCF is a bit=20 > costy...).=20 > > See description under=20 > http://www.gaussian.com/g_ur/k_guess.htm on the=20 > > bottom together with GUESS=3DALTER. This is not a=20 > particularly elegant=20 > > way to do things (compared to just specifying the state symmetry in=20 > > e.g. MOLPRO) but it works. You might want to use the STABLE=20 > option so=20 > > that you know whether you have instabilities to which other=20 > states and=20 > > which additional MO swaps you might want to perform. > > > > Best > > > > Johannes > > > > --------------------------------------------------------------- > > Johannes Hachmann > > (Dipl.-Chem., M.Sc.) > > > > Chan Research Group > > 140D Baker Laboratory > > Department of Chemistry and Chemical Biology Cornell University=20 > > Ithaca, NY 14853-1301 USA > > --------------------------------------------------------------- > >> -----Original Message----- > >> From: owner-chemistry+jh388=3D=3Dcornell.edu[]ccl.net > >> [mailto:owner-chemistry+jh388=3D=3Dcornell.edu[]ccl.net] On Behalf = Of=20 > >> xunlei ding dingxunlei::gmail.com > >> Sent: Friday, February 13, 2009 3:42 AM > >> To: Hachmann, Johannes > >> Subject: CCL:G: G- How to retain the symmetry in a SCF=20 > calculation ? > >> > >> > >> Sent to CCL by: xunlei ding [dingxunlei.:.gmail.com] Dear CCLers, > >> > >> In the manual of G03, the key word "SCF=3D Symm" is=20 > discribed as below: > >> Retain all symmetry constraints: make the number of=20 > occupied orbitals=20 > >> of each symmetry type (abelian irreducible > >> representation) match that of the initial guess. Use this=20 > option to=20 > >> retain a specific state of the wavefunction throughout the=20 > >> calculation. It is the default only for GVB calculations. > >> > >> But sometimes it doesn't work and the last state is different from=20 > >> the initial state. > >> > >> Could you give me more suggestions on how to retain the=20 > symmetry in a=20 > >> SCF calculation? > >> > >> Thanks! > >> > >> Best regards, > >> Ding > >> > >> > >> > >> -=3D This is automatically added to each message by the=20 > mailing script=20 > >> =3D- To recover the email address of the author of the=20 > message, please=20 > >> change the strange characters on the top line to the []=20 > sign. You can=20 > >> also>=20 > >> Conferences: > >> http://server.ccl.net/chemistry/announcements/conferences/ > >> > >> Search Messages: http://www.ccl.net/htdig (login: ccl, > >> Password: search)> > >> > > > > > > > > -=3D This is automatically added to each message by the=20 > mailing script=20 > > =3D-> Search Messages: http://www.ccl.net/htdig (login: ccl,=20 > Password:=20 > > search)> > > > > >=20 >=20 >=20 > -- > ------------------------------------------------------ > Xun-Lei Ding > Associate Research Professor of Physical Chemistry State Key=20 > Lab for Struct. Chem. of Unstable and Stable Species=20 > Institute of Chemistry, The Chinese Academy of Sciences=20 > Zhongguancun North First Street 2=EF=BC=8C > Beijing 100190, P. R. China > Phone 86-10-62568330 > Fax 86-10-62559373 >=20 >=20 >=20 > -=3Dhis is automatically added to each message by the mailing script = =3D > To recover the email address of the author of the message,=20 > please change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20