From owner-chemistry@ccl.net Thu Apr 23 02:51:00 2009 From: "Vincent Xianlong Wang xloongw+/-yahoo.com" To: CCL Subject: CCL:G: tailored redundant internal coordinates Message-Id: <-39138-090423023214-23323-CFYjEL0H+ZSG561nOz3BRg|-|server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Type: multipart/alternative; boundary="0-453102675-1240468321=:29298" Date: Wed, 22 Apr 2009 23:32:01 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw,,yahoo.com] --0-453102675-1240468321=:29298 Content-Type: text/plain; charset=us-ascii Hi Alexander, Have you solved your problem? I have done some studies on internal rotation of multiple functional groups in both isolated molecules and in cluster models. My solution to your problem is that I wrote some codes in Mathematica to output the molecules in a customized way instead of using GaussView or other tools. I tried the "ModRedundant" keywords when I started my projects, but never felt it was easy to use or fit my goal. If you are interested, I could share my codes with you and or build an input file for your molecules. Best regards, Vincent ________________________________ > From: Alexander Hoepker achoepker:-:gmail.com To: "Wang, Xianlong " Sent: Friday, April 17, 2009 3:56:32 AM Subject: CCL:G: tailored redundant internal coordinates Dear CCL community, My specific problem: Rotamers of diisopropyl groups (i-Pr)2 have become a troubling reality in numerous of my B3LYP geometry optimizations using Gaussian. It appears that the i-Pr groups cannot rotate past each other during the optimization presumably due to too high of a barrier. The optimizations therefore routinely misses rotamers of potentially lower energy. My question: Is it possible to redefine the redundant internal coordinates to include several key dihedral angles as structural parameters to more efficiently describe the i-Pr rotation. It has been suggested to me to use ModRedundant and simply add a structural parameter (such as bondlength, bondangle or dihedral angle) to the Z-Matrix. It would seem though, that this would only add parameters to the optimization process. By redefining the redundant internal coordinates while including the desired structural parameters, the geometry optimization may be improved. Could anybody comment on this and perhaps comment on software that would allow one to build user-defined redundant internal coordinates. Thanks in advance, Alexander Hoepker Cornell University Department of Chemistry and Chemical Biology --0-453102675-1240468321=:29298 Content-Type: text/html; charset=us-ascii
Hi Alexander,

Have you solved your problem?
I have done some studies on internal rotation of multiple functional groups in both isolated molecules and in cluster models.  My solution to your problem is that I wrote some codes in Mathematica to output the molecules in a customized way instead of using GaussView or other tools.  I tried the "ModRedundant" keywords when I started my projects, but never felt it was easy to use or fit my goal.
If you are interested, I could share my codes with you and or build an input file for your molecules.

Best regards,
Vincent

From: Alexander Hoepker achoepker:-:gmail.com <owner-chemistry * ccl.net>
To: "Wang, Xianlong " <xloongw * yahoo.com>
Sent: Friday, April 17, 2009 3:56:32 AM
Subject: CCL:G: tailored redundant internal coordinates

Dear CCL community,

My specific problem: Rotamers of diisopropyl groups (i-Pr)2 have become a troubling reality in numerous of my B3LYP geometry optimizations using Gaussian. It appears that the i-Pr groups cannot rotate past each other during the optimization presumably due to too high of a barrier. The optimizations therefore routinely misses rotamers of potentially lower energy.
My question: Is it possible to redefine the redundant internal coordinates to include several key dihedral angles as structural parameters to more efficiently describe the i-Pr rotation. It has been suggested to me to use ModRedundant and simply add a structural parameter (such as bondlength, bondangle or dihedral angle) to the Z-Matrix. It would seem though, that this would only add parameters to the optimization process. By redefining the redundant internal coordinates while including the desired structural parameters, the geometry optimization may be improved.

Could anybody comment on this and perhaps comment on software that would allow one to build user-defined redundant internal coordinates.

Thanks in advance,

Alexander Hoepker
Cornell University
Department of Chemistry and Chemical Biology


--0-453102675-1240468321=:29298-- From owner-chemistry@ccl.net Thu Apr 23 06:00:00 2009 From: "Sebastian Kozuch kozuchs#,#yahoo.com" To: CCL Subject: CCL: Computational Chemistry Wiki Message-Id: <-39139-090423051304-29114-AfekVybx4JLRcjO5vR2dCA[A]server.ccl.net> X-Original-From: Sebastian Kozuch Content-Type: multipart/alternative; boundary="0-1775155983-1240477969=:81893" Date: Thu, 23 Apr 2009 02:12:49 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [kozuchs]_[yahoo.com] --0-1775155983-1240477969=:81893 Content-Type: text/plain; charset=us-ascii Some days ago I asked if someone knows about a place where I can find updated information on computational chemistry methods. Apparently there isn't any web page that maintains this kind of data in a complete manner. Of course you have books (Cramer's "Essentials of computational chemistry" or Jensen's "Introduction to computational chemistry" as an example), and there's always reviews and benchmark papers. But I was looking for something really simple and updated. Books are updated up to the edition year. And let's face it, papers are a real pain in the neck if you just want a simple explanation. That's why I decided to try a new approach and opened a Wiki page where everyone can write and read about computational chemistry methods. This can include traditional methods (MM, HF, DFT, MD,...) or new ones, which implies that the authors of those methods are welcomed to make self-publicity. Writing a wiki article seems to be rather easy, but I'm not a specialist on the system or on methods, so the page is totally empty. If there are specialists out there that want to contribute to it, maybe it can be a usefull learning tool. I really hope for it. It is not intended to be a forum (we have CCL for that). Just a place we can find usefull, updated and SIMPLE information. The page is: http://computationalchemistry.wikia.com xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ..........Sebastian Kozuch........... xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ...The Lise Meitner-Minerva Center... .for Computational Quantum Chemistry. ...Hebrew University of Jerusalem.... .....kozuchs:_:yfaat.ch.huji.ac.il..... http://yfaat.ch.huji.ac.il/kozuch.htm xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --0-1775155983-1240477969=:81893 Content-Type: text/html; charset=us-ascii
Some days ago I asked if someone knows about a place where I can find updated information on computational chemistry methods. Apparently there isn't any web page that maintains this kind of data in a complete manner. Of course you have books (Cramer's "Essentials of computational chemistry" or Jensen's "Introduction to computational chemistry" as an example), and there's always reviews and benchmark papers. But I was looking for something really simple and updated. Books are updated up to the edition year. And let's face it, papers are a real pain in the neck if you just want a simple explanation.
That's why I decided to try a new approach and opened a Wiki page where everyone can write and read about computational chemistry methods. This can include traditional methods (MM, HF, DFT, MD,...) or new ones, which implies that the authors of those methods are welcomed to make self-publicity.
Writing a wiki article seems to be rather easy, but I'm not a specialist on the system or on methods, so the page is totally empty. If there are specialists out there that want to contribute to it, maybe it can be a usefull learning tool. I really hope for it.
It is not intended to be a forum (we have CCL for that). Just a place we can find usefull, updated and SIMPLE information.

The page is:

http://computationalchemistry.wikia.com


 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
...The Lise Meitner-Minerva Center...
.for Computational Quantum Chemistry.
...Hebrew University of Jerusalem....
.....kozuchs:_:yfaat.ch.huji.ac.il.....
http://yfaat.ch.huji.ac.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx


--0-1775155983-1240477969=:81893-- From owner-chemistry@ccl.net Thu Apr 23 07:54:00 2009 From: "Rzepa, Henry h.rzepa**imperial.ac.uk" To: CCL Subject: CCL: Computational Chemistry Wiki Message-Id: <-39140-090423072234-30301-XaIfD05ozq7VN1FcwXffMg[]server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Thu, 23 Apr 2009 11:37:54 +0100 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa]|[imperial.ac.uk] > >That's why I decided to try a new approach and opened a Wiki page where everyone can write and read about computational chemistry methods. This can include traditional methods (MM, HF, DFT, MD,...) or new ones, which implies that the authors of those methods are welcomed to make self-publicity. There is also the blog approach. A good example is Steve Bachrach's blog, which is in fact coupled to his own textbook on computational chemistry, and which Steve tells me he regards in some ways as a running update to that book; http://hackberry.chem.trinity.edu/blog/ It too can be annotated with comments from others, and several good examples of such annotation can be seen there currently. It should be noted that in terms of authoring tools, the blog approach is less flexible than the Wiki approach. Finally, I venture to suggest that many of the modern computational chemistry methods are also to be found on the Wikipedia pages, where they are lovingly curated by a devoted team. Because cross-referencing is so easy in a Wiki, I tend to think that the more comprehensive the Wiki pages are, the better. In that sense, fragmenting computational chemistry across many diverse wikis is probably less desirable. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); http://www.ch.ic.ac.uk/rzepa/blog/ http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Thu Apr 23 08:40:00 2009 From: "Lukasz Cwiklik cwiklik]^[gmail.com" To: CCL Subject: CCL: Computational Chemistry Wiki Message-Id: <-39141-090423083757-23850-HygKmlyGBw6FoQNriwRIQQ-#-server.ccl.net> X-Original-From: Lukasz Cwiklik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 23 Apr 2009 15:37:43 +0300 MIME-Version: 1.0 Sent to CCL by: Lukasz Cwiklik [cwiklik..gmail.com] Dear Sebastian, I do not want to undermine your idea of a new wiki, however, this kind of wiki exist, it is simply in Wikipedia (see 'Computational Chemistry' article which covers a similar range of topics: http://en.wikipedia.org/wiki/Computational_chemistry). So maybe it would be better and easier to encourage CCL-ers to extend the existing Wikipedia articles in this topic. Also, the resulting information would be much more accessible for the general audience. Anyway, your idea to convince people to write something in the wiki system is very good. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com On Thu, Apr 23, 2009 at 12:12 PM, Sebastian Kozuch kozuchs#,#yahoo.com wrote: > Some days ago I asked if someone knows about a place where I can find > updated information on computational chemistry methods. Apparently there > isn't any web page that maintains this kind of data in a complete manner. Of > course you have books (Cramer's "Essentials of computational chemistry" or > Jensen's "Introduction to computational chemistry" as an example), and > there's always reviews and benchmark papers. But I was looking for something > really simple and updated. Books are updated up to the edition year. And > let's face it, papers are a real pain in the neck if you just want a simple > explanation. > That's why I decided to try a new approach and opened a Wiki page where > everyone can write and read about computational chemistry methods. This can > include traditional methods (MM, HF, DFT, MD,...) or new ones, which implies > that the authors of those methods are welcomed to make self-publicity. > Writing a wiki article seems to be rather easy, but I'm not a specialist on > the system or on methods, so the page is totally empty. If there are > specialists out there that want to contribute to it, maybe it can be a > usefull learning tool. I really hope for it. > It is not intended to be a forum (we have CCL for that). Just a place we can > find usefull, updated and SIMPLE information. > > The page is: > > http://computationalchemistry.wikia.com > > > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > ..........Sebastian Kozuch........... > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > ...The Lise Meitner-Minerva Center... > .for Computational Quantum Chemistry. > ...Hebrew University of Jerusalem.... > .....kozuchs]_[yfaat.ch.huji.ac.il..... > http://yfaat.ch.huji.ac.il/kozuch.htm > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > > From owner-chemistry@ccl.net Thu Apr 23 09:15:01 2009 From: "senthil kumar l lsenthil_kumar++rediffmail.com" To: CCL Subject: CCL:G: gausian 03 software Message-Id: <-39142-090423081211-9979-kE6HsFgQB4BnX5brtgHYUA=-=server.ccl.net> X-Original-From: "senthil kumar l" Date: Thu, 23 Apr 2009 08:12:07 -0400 Sent to CCL by: "senthil kumar l" [lsenthil_kumar**rediffmail.com] hello everone I would like to know how to get S and F matrix from Gaussian03 calculations (i donot have source code) to analyse charge transfer.Has any one tried it please let me know. bye From owner-chemistry@ccl.net Thu Apr 23 09:49:00 2009 From: "=?ISO-8859-1?Q?Philippe_Carbonni=E8re?= philippe.carbonniere%a%univ-pau.fr" To: CCL Subject: CCL: computational aspects of the modelling of vibrational properties, ICCMSE 2009 Message-Id: <-39143-090423093920-19448-gJADWNu+w7lV7UmDzyF2rQ^server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Philippe_Carbonni=E8re?= Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 23 Apr 2009 15:38:51 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Philippe_Carbonni=E8re?= [philippe.carbonniere##univ-pau.fr] "Computational aspects of the modelling of vibrational properties of gases, liquids and solids" This international symposium will be held in the conference: "Seventh International Conference of Computational Methods in Sciences and Engineering" (http://www.iccmse.org/) at Hotel Rodos Palace, Rhodes, Crete, Greece. from September 29 to October 4, 2009. The interested participants are invited to submit their abstracts. Organizers : Philippe Carbonniere and Claude Pouchan, IPREM, Pau University, France and Mauro Causa, University "Federico II", Naples, Italy Contact philippe.carbonniere[*]univ-pau.fr Scope : Vibrational spectroscopy is a particularly powerful tool for non-destructive characterisation of molecular systems. Besides routine analysis in a wide range of domains (food science, archaeology, astrophysics, medicine),numerous applications in molecular science, such as speciation, conformational analysis, molecular design and reactivity monitoring, can be based on the modelling of vibrational effects. In recent years computational chemistry provides powerful tools for the modelling of such properties in the gas, liquid and solid phase although anharmonicity, resonances, environmental and dynamic effects render the problem non-trivial. Several computational aspects will be emphasised in the present symposium: the quality of the potential electronic surface, time-dependent and time-independent approaches to the study of vibration, the treatment of the condensed phases (solvent, surfaces and bulk), the computation of intensities and possible ways to overcome actual limitations due to the size of the treated systems. From owner-chemistry@ccl.net Thu Apr 23 10:41:00 2009 From: "Moreau Yohann yohann.moreau=-=lcp.u-psud.fr" To: CCL Subject: CCL:G: gausian 03 software Message-Id: <-39144-090423104022-30764-NNcuKTMm5Hn6Q/U/s6rWsg|,|server.ccl.net> X-Original-From: Moreau Yohann Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-15" Date: Thu, 23 Apr 2009 16:40:19 +0200 MIME-Version: 1.0 Sent to CCL by: Moreau Yohann [yohann.moreau],[lcp.u-psud.fr] Hi,=20 A solution is to add iop(x/33=3Dn) to your keywords. =20 where x is the number of the overlay and n refers to the level of verbosity. As far as I remember, S is computed in overlay 3, hence, with x=3D3 and n= =3D3, you=20 should get the S matrix in lower triangular form expressed in the basis of= =20 atomic orbitals (as far as I remember). =46or the F matrix, things may happen in overlay 5 (SCF calculations are ma= de in=20 link 502). Anyway a quick look at=20 http://gaussian.com/iops.htm should provide you more detailed information about this IOP number. Please notice the output can dramatically increase. Hope this helps, Regards,=20 Yohann Le jeudi 23 avril 2009 14:12:07 senthil kumar l=20 lsenthil_kumar++rediffmail.com, vous avez =E9crit : > Sent to CCL by: "senthil kumar l" [lsenthil_kumar**rediffmail.com] > hello everone > > I would like to know how to get S and F matrix from Gaussian03 calculatio= ns > (i donot have source code) to analyse charge transfer.Has any one tried it > please let me know. > > bye > > > > -=3D This is automatically added to each message by the mailing script = =3D-=2D-=20 Yohann Moreau Laboratoire de Chimie Physique Universit=E9 de Paris-Sud B=E2timent 349 91405 Orsay cedex =46rance Tel : +33 (0) 1 69 15 73 98 =46ax :+33 (0) 1 69 15 61 88 From owner-chemistry@ccl.net Thu Apr 23 12:33:01 2009 From: "Rajagopalan S. r.subramanian ~~ ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: gausian 03 software Message-Id: <-39145-090423123119-4922-mRUrwddZPKD1zs/G7shebA###server.ccl.net> X-Original-From: "Rajagopalan S." Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 23 Apr 2009 18:31:04 +0200 MIME-Version: 1.0 Sent to CCL by: "Rajagopalan S." [r.subramanian]*[ipc.uni-stuttgart.de] Hi, use the keyword 'iop(7/33=1)' before 'freq'. it will print the following (everything in order) 1. Hessian after L701 (1+2+3+...+3N), 2.cart. force constants i.e., Hessain after L703 (1+2+3+...+3N), 3. force constants in cart. coordinates (1+2+3+...+3N), 4. internal force constants (1+2+3+...+(3N-6)), 5. force constants in internal coordinates (1+2+3+...+(3N-6)). PS: if you need only 2 just save the checkpointfile without using iop(7/33=1). 2 will be save in chk file. Moreau Yohann yohann.moreau=-=lcp.u-psud.fr wrote: > Sent to CCL by: Moreau Yohann [yohann.moreau],[lcp.u-psud.fr] > Hi, > > A solution is to add iop(x/33=n) to your keywords. > > where x is the number of the overlay and n refers to the level of verbosity. > As far as I remember, S is computed in overlay 3, hence, with x=3 and n=3, you > should get the S matrix in lower triangular form expressed in the basis of > atomic orbitals (as far as I remember). > For the F matrix, things may happen in overlay 5 (SCF calculations are made in > link 502). > Anyway a quick look at > http://gaussian.com/iops.htm > should provide you more detailed information about this IOP number. > > Please notice the output can dramatically increase. > Hope this helps, > > Regards, > > Yohann > > > > > Le jeudi 23 avril 2009 14:12:07 senthil kumar l > lsenthil_kumar++rediffmail.com, vous avez écrit : > >> Sent to CCL by: "senthil kumar l" [lsenthil_kumar**rediffmail.com] >> hello everone >> >> I would like to know how to get S and F matrix from Gaussian03 calculations >> (i donot have source code) to analyse charge transfer.Has any one tried it >> please let me know. >> >> bye-- >> > Yohann Moreau > Laboratoire de Chimie Physique > Université de Paris-Sud > Bâtiment 349 > 91405 Orsay cedex > France > > Tel : +33 (0) 1 69 15 73 98 > Fax :+33 (0) 1 69 15 61 88 > > > > -=his is automatically added to each message by the mailing script =-> > > From owner-chemistry@ccl.net Thu Apr 23 13:07:01 2009 From: "richard apodaca rich_apodaca_._yahoo.com" To: CCL Subject: CCL:G: Making movies from molecular vibrations easily Message-Id: <-39146-090422101349-31926-PDFeIg+A/R0l5puyy2AnmA+*+server.ccl.net> X-Original-From: richard apodaca Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 22 Apr 2009 06:13:36 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: richard apodaca [rich_apodaca _ yahoo.com] Hello Thomas,=0A=0AThis isn't really my area, but I ran across this: "Easil= y Make a Movie with PyMOL":=0A=0Ahttp://www.p212121.com/2009/03/24/easily-m= ake-movie-pymol/=0A=0AIf it doesn't answer you question directly, it might = have some useful leads.=0A=0AGood luck,=0ARich=0A=0A_______________________= ____________=0A=0ARichard L. Apodaca=0A=0Ahttp://depth-first.com Blog= =0Ahttp://metamolecular.com Company=0A=0A=0A--- On Wed, 4/22/09, Sten Ni= lsson Lill stenil ~ chem.gu.se wrote:=0A=0A> From= : Sten Nilsson Lill stenil ~ chem.gu.se =0A> Subje= ct: CCL:G: Making movies from molecular vibrations easily=0A> To: "Apodaca,= Rich " =0A> Date: Wednesday, April 22, 200= 9, 1:59 AM=0A> =0A> Sent to CCL by: "Sten Nilsson Lill" [stenil|*|chem.gu.s= e]=0A> Dear Thomas,=0A> =0A> Chemcraft has this feature and it works perfec= tly OK to use=0A> it in e.g.=0A> PowerPoint presentations. It reads Gaussia= n frequency=0A> calculations, but=0A> not Turbomole calculations as far as = I know.=0A> =0A> Please look at http://www.chemcraftprog.com/ for the=0A> d= etails.=0A> =0A> Hope it helps,=0A> =0A> Sten=0A> =0A> =0A> >=0A> > Sent to= CCL by: "Dipl.-Ing. Thomas Mitterfellner"=0A> > [thomas.mitterfellner^^^tu= graz.at]=0A> > Hello!=0A> >=0A> > I've been searching through the web and t= hrough the=0A> archives but I=0A> > couldn't find a decent solution for mak= ing a movie of=0A> a molecular=0A> > vibration one gets from a frequency ca= lculation with=0A> Gaussian or=0A> > Turbomole. While Gaussview, Molden, Mo= lekel and Jmol=0A> (no imaginary=0A> > modes, as it seems!), are able to di= splay the=0A> vibrations, there is no=0A> > easy option to create, say an a= nimated GIF (with=0A> transparency!), or an=0A> > MPEG.=0A> > How do you go= about animating molecular vibrations for=0A> insertion into a=0A> > presen= tation? I'd appreciate any help (preferably, but=0A> not limited to=0A> > l= inux/OSS solutions)!=0A> >=0A> > Thank you,=0A> >=0A> > Thomas>=0A> >=0A> >= =0A> =0A> =0A> Ph. D. Sten Nilsson Lill=0A> Dep. of Chemistry=0A> Universit= y of Gothenburg=0A> Kemig=E5rden 4=0A> S-412 96 G=F6teborg, Sweden=0A> Phon= e: +46-31-772 2873=0A> Fax: +46-31-772 3840=0A> E-mail: stenil[*]chem.gu.se= =0A> Alternative e-mail: stenil[*]physto.se=0A> =0A> =0A> =0A> -=3D This is= automatically added to each message by the=0A> mailing script =3D-=0A> To = recover the email address of the author of the message,=0A> please change= =0A> the strange characters on the top line to the --- sign. You=0A> can also= =0A=0A> =0A> E-mail = to subscribers: CHEMISTRY---ccl.net=0A> or use:=0A> =A0 =A0 =A0 http://www.cc= l.net/cgi-bin/ccl/send_ccl_message=0A> =0A> E-mail to administrators: CHEMI= STRY-REQUEST---ccl.net=0A> or use=0A> =A0 =A0 =A0 http://www.ccl.net/cgi-bin/= ccl/send_ccl_message=0A> =0A=0A> =A0 =A0 =A0 http:= //www.ccl.net/chemistry/sub_unsub.shtml=0A> =0A> Before posting, check wait= time at: http://www.ccl.net=0A> =0A=0A> Con= ferences: http://server.ccl.net/chemistry/announcements/conferences/=0A> = =0A=0A= > =0A=0A> =A0 =A0 = =A0=0A> =0A> RTFI: http://www.ccl.net/chemi= stry/aboutccl/instructions/=0A> =0A> =0A> From owner-chemistry@ccl.net Thu Apr 23 13:44:00 2009 From: "Roman D Gorbunov rgorbuno]![aecom.yu.edu" To: CCL Subject: CCL:G: Ab initio Geometry Optimization Message-Id: <-39147-090423125611-16354-j8ppfD0XmOM3I47Sop+tSQ^_^server.ccl.net> X-Original-From: "Roman D Gorbunov" Date: Thu, 23 Apr 2009 12:56:08 -0400 Sent to CCL by: "Roman D Gorbunov" [rgorbuno..aecom.yu.edu] Dear CCL Subscribers, I have a problem with the convergence of a partial geometry optimization (with the Gaussian). First 100 steps everything goes OK, total energy and RMS gradient smoothly decrease. After 100 steps the total energy and RMS gradients start to "jump". This "random jumping" continues for next 200 steps and in the end I have the "error termination" of the Gaussian. Can anybody pleas give me some hints how to deal with this problem? I could try to increase the "MaxCycle". But, I think, it makes sense to prolongate the geometry optimization if I have a continues improvement of the geometry (which does not seems to be my case). I thought about the usage of the "CalcAll" but I have a rather big system and it will be too time consuming. The last solution which comes into my mind is to try different initial geometries. Does anybody know some other ways to deal with the geometry convergence problem? Thank you in advance, Roman From owner-chemistry@ccl.net Thu Apr 23 15:18:00 2009 From: "Nir London nir{}rosettadesigngroup.com" To: CCL Subject: CCL: What is your favorite journal in the field of computational structural Message-Id: <-39148-090423151503-32353-KMmj1xpvxrvus0y+HrnbmQ|*|server.ccl.net> X-Original-From: "Nir London" Date: Thu, 23 Apr 2009 15:14:59 -0400 Sent to CCL by: "Nir London" [nir:rosettadesigngroup.com] Of course were all reading all of the journals below, and certainly each has its own benefits. There is also the question if by favorite journal we mean where would you like to publish, or which are you enjoying reading the most? We know the question isnt adequately defined. Nontheless, we urge you to pick one and try to explain in the comments what makes that journal special. http://rosettadesigngroup.com/blog/353/what-is-your-favorite-journal-in-the-field-of- computational-structural-biology/ Nir. From owner-chemistry@ccl.net Thu Apr 23 16:03:01 2009 From: "Farhan Pasha pashafa|*|yahoo.co.in" To: CCL Subject: CCL:G: Making movies from molecular vibrations easily Message-Id: <-39149-090423081123-9357-VBVu2qo9k81j5OWJ+jl0vw[]server.ccl.net> X-Original-From: Farhan Pasha Content-Type: multipart/alternative; boundary="0-1324744680-1240488666=:57609" Date: Thu, 23 Apr 2009 17:41:06 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Farhan Pasha [pashafa%yahoo.co.in] --0-1324744680-1240488666=:57609 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable for the reaction coordinates you=A0 can make a mpeg format movie in maestro Correspondence Address =0ADr. Syed Farhan Ahmad Pasha =0ARoom No. 5202 =0AInstitut de Biologie Structurale =0ALaboratoire de Dynamique Moleculaire =0A41 rue Jules Horowitz =0A38027 Grenoble cedex =0AFrance =0Atel : (+33) (0)4 38 78 99 28 =0Afax : (+33) (0)4 38 78 54 94 =0Afpasha#%#rediffmail.com =0AURL:www.geocities.com/pashafa =0Awww.ibs.fr --- On Wed, 22/4/09, Danni Harris danni:_:simbiosys.ca wrote: > From: Danni Harris danni:_:simbiosys.ca Subject: CCL:G: Making movies from molecular vibrations easily To: "Pasha, Frahan Ahmad " Date: Wednesday, 22 April, 2009, 7:10 PM Sent to CCL by: "Danni Harris" [danni###simbiosys.ca] Thomas---I don't know of an application for viewing QM output of e.g. reaction coordinate or vibration animation ----that will output a movie directly but there is an application GIFMERGE that will take an output of GIF's from any viewer (e.g. molden) and merge them into a GIF animation. I forget whether there is a transparency feature...but check this out: http://the-labs.com/GIFMerge/ Danni > > Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" > [thomas.mitterfellner^^^tugraz.at] > Hello! > > I've been searching through the web and through the archives but I > couldn't find a decent solution for making a movie of a molecular > vibration one gets from a frequency calculation with Gaussian or > Turbomole. While Gaussview, Molden, Molekel and Jmol (no imaginary > modes, as it seems!), are able to display the vibrations, there is no > easy option to create, say an animated GIF (with transparency!), or an > MPEG. > How do you go about animating molecular vibrations for insertion into a > presentation? I'd appreciate any help (preferably, but not limited to > linux/OSS solutions)! > > Thank you, > > Thomas> > --=20 Danni Harris, Ph.D. Scientific Sales and Support Executive Computational Chemistry Software Development SimBioSys 135 Queens Plate Dr.; Unit 520 Toronto, Ontario M9W V61, Canada Tel. Head-Office: 416-741-4263 Mobile: 650-799-6637 Fax: 416-741-5084 Web: http://www.simbiosys.ca -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A Bring your gang together. Do your thing. Find your favourite= Yahoo! group at http://in.promos.yahoo.com/groups/ --0-1324744680-1240488666=:57609 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable <= /table>
=0A=0A=0A
Bollywood news, movie = reviews, film trailers and more! Click here. --0-1324744680-1240488666=:57609-- From owner-chemistry@ccl.net Thu Apr 23 16:40:00 2009 From: "Duy Le ttduyle*o*gmail.com" To: CCL Subject: CCL:G: Ab initio Geometry Optimization Message-Id: <-39150-090423155901-21669-IT5yU+aQlyxYptlx98PlNA:+:server.ccl.net> X-Original-From: Duy Le Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 23 Apr 2009 15:28:32 -0400 MIME-Version: 1.0 Sent to CCL by: Duy Le [ttduyle]*[gmail.com] Dear there, I'll start with low theory level optimization (am1, HF...) or small basis set. After that, start to increase theory level and/or basis set to your need. best luck. D. On Thu, Apr 23, 2009 at 12:56 PM, Roman D Gorbunov rgorbuno]![aecom.yu.edu wrote: > > Sent to CCL by: "Roman D Gorbunov" [rgorbuno..aecom.yu.edu] > Dear CCL Subscribers, > > I have a problem with the convergence of a partial geometry optimization = (with the Gaussian). First 100 steps everything goes OK, total energy and R= MS gradient smoothly decrease. After 100 steps the total energy and RMS gra= dients start to "jump". This "random jumping" continues for next 200 steps = and in the end I have the "error termination" of the Gaussian. > > Can anybody pleas give me some hints how to deal with this problem? I cou= ld try to increase the "MaxCycle". But, I think, it makes sense to prolonga= te the geometry optimization if I have a continues improvement of the geome= try (which does not seems to be my case). > > I thought about the usage of the "CalcAll" but I have a rather big system= and it will be too time consuming. > > The last solution which comes into my mind is to try different initial ge= ometries. > > Does anybody know some other ways to deal with the geometry convergence p= roblem? > > Thank you in advance, > Roman > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Men don't need hands to do things! From owner-chemistry@ccl.net Thu Apr 23 17:13:00 2009 From: "Duy Le ttduyle*_*gmail.com" To: CCL Subject: CCL:G: Making movies from molecular vibrations easily Message-Id: <-39151-090423162039-5436-3OIKaVGVXUgZw/fRa4qjUw|*|server.ccl.net> X-Original-From: Duy Le Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 23 Apr 2009 15:25:05 -0400 MIME-Version: 1.0 Sent to CCL by: Duy Le [ttduyle]![gmail.com] Hello there, It will not be big headache if we just use simple way: - make pictures for all frames we want to display in movie - Use any gif maker or movie maker to create .GIF animation or Movie. *Gif maker: Excellent one http://linux.maruhn.com/sec/whirlgif.html Photoshop *Moviemaker: Simplest one WINDOWS MOVIE MAKER Other movie maker which can make movie from pictures. Regards, D. On Wed, Apr 22, 2009 at 9:13 AM, richard apodaca rich_apodaca_._yahoo.com wrote: > > Sent to CCL by: richard apodaca [rich_apodaca _ yahoo.com] > > > Hello Thomas, > > This isn't really my area, but I ran across this: "Easily Make a Movie wi= th PyMOL": > > http://www.p212121.com/2009/03/24/easily-make-movie-pymol/ > > If it doesn't answer you question directly, it might have some useful lea= ds. > > Good luck, > Rich > > ___________________________________ > > Richard L. Apodaca > > http://depth-first.com =A0 =A0 =A0Blog > http://metamolecular.com =A0 =A0Company > > > --- On Wed, 4/22/09, Sten Nilsson Lill stenil ~ chem.gu.se wrote: > >> From: Sten Nilsson Lill stenil ~ chem.gu.se >> Subject: CCL:G: Making movies from molecular vibrations easily >> To: "Apodaca, Rich " >> Date: Wednesday, April 22, 2009, 1:59 AM >> >> Sent to CCL by: "Sten Nilsson Lill" [stenil|*|chem.gu.se] >> Dear Thomas, >> >> Chemcraft has this feature and it works perfectly OK to use >> it in e.g. >> PowerPoint presentations. It reads Gaussian frequency >> calculations, but >> not Turbomole calculations as far as I know. >> >> Please look at http://www.chemcraftprog.com/ for the >> details. >> >> Hope it helps, >> >> Sten >> >> >> > >> > Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" >> > [thomas.mitterfellner^^^tugraz.at] >> > Hello! >> > >> > I've been searching through the web and through the >> archives but I >> > couldn't find a decent solution for making a movie of >> a molecular >> > vibration one gets from a frequency calculation with >> Gaussian or >> > Turbomole. While Gaussview, Molden, Molekel and Jmol >> (no imaginary >> > modes, as it seems!), are able to display the >> vibrations, there is no >> > easy option to create, say an animated GIF (with >> transparency!), or an >> > MPEG. >> > How do you go about animating molecular vibrations for >> insertion into a >> > presentation? I'd appreciate any help (preferably, but >> not limited to >> > linux/OSS solutions)! >> > >> > Thank you, >> > >> > Thomas> >> > >> > >> >> >> Ph. D. Sten Nilsson Lill >> Dep. of Chemistry >> University of Gothenburg >> Kemig=E5rden 4 >> S-412 96 G=F6teborg, Sweden >> Phone: +46-31-772 2873 >> Fax: +46-31-772 3840 >> E-mail: stenil[*]chem.gu.se >> Alternative e-mail: stenil[*]physto.se >> >> >> >> -=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 > >> >> E-mail to subscribers: CHEMISTRY_+_ccl.net >> or use: >> =A0 =A0 =A0>> >> E-mail to administrators: CHEMISTRY-REQUEST_+_ccl.net >> or use >> =A0 =A0 =A0>> > >> =A0 =A0 =A0>> >> >> > > > > - This is automatically added to each message by the mailing script -> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Men don't need hands to do things! From owner-chemistry@ccl.net Thu Apr 23 19:10:00 2009 From: "Brian Salter-Duke brian.james.duke---gmail.com" To: CCL Subject: CCL: Computational Chemistry Wiki Message-Id: <-39152-090423190314-23293-ZwLwkEEX84pIn/wNYsdY1A(~)server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 24 Apr 2009 09:02:53 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke:-:gmail.com] Lukasz Cwiklik cwiklik]^[gmail.com wrote: > Sent to CCL by: Lukasz Cwiklik [cwiklik..gmail.com] > Dear Sebastian, > I do not want to undermine your idea of a new wiki, however, this kind > of wiki exist, it is simply in Wikipedia (see 'Computational > Chemistry' article which covers a similar range of topics: > http://en.wikipedia.org/wiki/Computational_chemistry). So maybe it > would be better and easier to encourage CCL-ers to extend the existing > Wikipedia articles in this topic. Also, the resulting information > would be much more accessible for the general audience. > Anyway, your idea to convince people to write something in the wiki > system is very good. > Best, > Lukasz > I word of caution about using wikipedia for the purposes proposed by the original poster of this thread, from one of the people Henry referred to who tries to upgrade, improve and protect the wikipedia articles on computational chemistry. Wipedia has its own policies and guidelines. We are writing an encyclopis based on what others have said. Everything should be referenced. Original research is not allowed. So "new ones, which implies that the authors of those methods are welcomed to make self-publicity" is an absolute no-no. Anyone trying to do that, would experience serious grief, with the material being promptly removed by someone, possibly me. There is also the science wiki, which was the original a computational chemistry wiki, as you can see from the URL it still has. Here is the main QC entry point:- http://www.compchemwiki.org/index.php?title=Quantum_chemistry The original purpose was rather different from what is suggested here, as it was to collect together QC results. It also not very active. I would encourage readers of CCL to help maintain and develop the wikipedia pages, but I suggest you move in slowly and learn how the place works. One problem with the CC and QC articles is that are often dominated by physicists and become almost unintelligible to chemists. They need to cover both physics and chemistry viewpoints. I sometimes give up on these articles and edit something completely different as a break from CC. I am happy to assist anyone. I am User:Bduke on wikipedia. Brian.
for the reaction coordinates you  can ma= ke a mpeg format movie in maestro

Correspondence Address
=0ADr. S= yed Farhan Ahmad Pasha
=0ARoom No. 5202
=0AInstitut de Biologie Struc= turale
=0ALaboratoire de Dynamique Moleculaire
=0A41 rue Jules Horowi= tz
=0A38027 Grenoble cedex
=0AFrance
=0Atel : (+33) (0)4 38 78 99 = 28
=0Afax : (+33) (0)4 38 78 54 94
=0Afpasha#%#rediffmail.com
=0AURL= :www.geocities.com/pashafa
=0Awww.ibs.fr

--- On Wed, 22/4/09, = Danni Harris danni:_:simbiosys.ca <owner-chemistry#%#ccl.net> wrote:

From: Danni Harris danni:_:simbios= ys.ca <owner-chemistry#%#ccl.net>
Subject: CCL:G: Making movies from= molecular vibrations easily
To: "Pasha, Frahan Ahmad " <pash= afa#%#yahoo.co.in>
Date: Wednesday, 22 April, 2009, 7:10 PM


Sent to CCL by: "Danni Harris" [danni###simbiosys.= ca]
Thomas---I don't know of an application for viewing QM output of e.g= .
reaction coordinate or vibration animation ----that will output a movi= e
directly but there is an application GIFMERGE that will take an output= of
GIF's from any viewer (e.g. molden) and merge them into a GIF animat= ion.
I forget whether there is a transparency feature...but check this o= ut:

http://the-labs.c= om/GIFMerge/

Danni
>
> Sent to CCL by: "Dipl.-Ing. T= homas Mitterfellner"
> [thomas.mitterfellner^^^tugraz.at]
> Hel= lo!
>
> I've been searching through the web and through the arc= hives but I
> couldn't find a decent solution for making a movie of a= molecular
> vibration one gets from a frequency calculation with Gau= ssian or
> Turbomole. While Gaussview, Molden, Molekel and Jmol (no i= maginary
> modes, as it seems!), are able to display the vibrations, = there is no
> easy option to create, say an animated GIF (with transp= arency!), or an
> MPEG.
> How do you go about animating molecul= ar vibrations for insertion into a
> presentation? I'd appreciate any= help (preferably, but not limited to
> linux/OSS solutions)!
>=
> Thank you,
>
> Thomas>
>


--
Danni Harris, Ph.D.
Scientific Sales and Support Executive
Compu= tational Chemistry Software Development
SimBioSys
135 Queens Plate Dr= .; Unit 520
Toronto, Ontario
M9W V61, Canada
Tel. Head-Office: 416= -741-4263
Mobile: 650-799-6637
Fax: 416-741-5084
Web: http://www.simbiosys.ca


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