From owner-chemistry@ccl.net Sun Jan 30 10:40:00 2011 From: "Ehsan shakerzadeh ehsan_shakerzadeh() yahoo.com" To: CCL Subject: CCL: Maximum Force and RMS force not coverged. What should I do? Message-Id: <-43798-110130060928-25746-g1wi6jzsjRKIgN5AsQeazA|server.ccl.net> X-Original-From: "Ehsan shakerzadeh" Date: Sun, 30 Jan 2011 06:09:27 -0500 Sent to CCL by: "Ehsan shakerzadeh" [ehsan_shakerzadeh|*|yahoo.com] Dear All, I run a job for a week. after a week Maximum Displacement and RMS Displacement are converged but Maximum Force and RMS force are not converged.some last SCF steps are also appered: SCF Done: E(RB+HF-LYP) = -3193.08688985 A.U. after 17 cycles SCF Done: E(RB+HF-LYP) = -3193.09622481 A.U. after 12 cycles SCF Done: E(RB+HF-LYP) = -3193.09657987 A.U. after 16 cycles SCF Done: E(RB+HF-LYP) = -3193.09662031 A.U. after 9 cycles SCF Done: E(RB+HF-LYP) = -3193.09662458 A.U. after 8 cycles SCF Done: E(RB+HF-LYP) = -3193.09662526 A.U. after 6 cycles SCF Done: E(RB+HF-LYP) = -3193.09662536 A.U. after 4 cycles SCF Done: E(RB+HF-LYP) = -3193.08688985 A.U. after 17 cycles SCF Done: E(RB+HF-LYP) = -3193.09622481 A.U. after 12 cycles SCF Done: E(RB+HF-LYP) = -3193.09657987 A.U. after 16 cycles SCF Done: E(RB+HF-LYP) = -3193.09662031 A.U. after 9 cycles SCF Done: E(RB+HF-LYP) = -3193.09662458 A.U. after 8 cycles SCF Done: E(RB+HF-LYP) = -3193.09662526 A.U. after 6 cycles SCF Done: E(RB+HF-LYP) = -3193.09662536 A.U. after 6 cycles SCF Done: E(RB+HF-LYP) = -3193.08688994 A.U. after 17 cycles SCF Done: E(RB+HF-LYP) = -3193.09622477 A.U. after 12 cycles SCF Done: E(RB+HF-LYP) = -3193.09657986 A.U. after 16 cycles SCF Done: E(RB+HF-LYP) = -3193.09662030 A.U. after 9 cycles SCF Done: E(RB+HF-LYP) = -3193.09662457 A.U. after 8 cycles SCF Done: E(RB+HF-LYP) = -3193.09662526 A.U. after 6 cycles SCF is converged but again go to first step. I would be pleased if anyone can help me to remove this problem. Thanks in advance. Ehsan From owner-chemistry@ccl.net Sun Jan 30 14:28:00 2011 From: "Patrick Bultinck patrick.bultinck##ugent.be" To: CCL Subject: CCL:G: Solving linear dependence in Gaussian with IOp(3/59) Message-Id: <-43799-110129144112-27401-R1CsKOF+OEeWbDuDFb9dag],[server.ccl.net> X-Original-From: Patrick Bultinck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Sat, 29 Jan 2011 20:40:52 +0100 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Patrick Bultinck [patrick.bultinck . ugent.be] Good question. The approach I take is a simple one. Punch the overlap matrix and compute the eigenvectors and eigenvalues. The linear dependence means that you have an eigenvector with a very low eigenvalue (you could say that the overlap matrix is no longer positive definite). Check this eigenvector and this will teach you a lot. If you are lucky, the eigenvector will give you a hint what basis function to remove from the basis set (take the one that has the largest coefficient). Then try again. If necessary repeat this procedure until the overlap matrix is positive definite. This is, in my experience, the only correct way to go. Ad hoc solutions are very tricky. If you take for example 6-311++G** and use some standard trick for removing the troublemaker eigenvector for conformation X and you use the same basis set for a conformation Y without overlap matrix issues, comparisons of properties are like comparing apples and oranges. If you do some manual work as I describe you can make sure you have the same basis for every conformation. Patrick ------------------------------------------ Prof. Dr. Patrick Bultinck Ghent Quantum Chemistry Group Dept. Inorganic and Physical Chemistry Ghent University Krijgslaan 281 (S3) 9000 Gent Belgium Tel : +32/9/2644423 Fax : +32/9/264.49.83 Patrick.Bultinck_+_UGent.be www.quantum.ugent.be www.chem.ugent.be/EN/exchangestudents On 27 Jan 2011, at 00:24, Ron Bakus rbakus+*+chem.ucsb.edu wrote: > > Sent to CCL by: "Ron Bakus" [rbakus() chem.ucsb.edu] > I typically work with large pi-conjugated systems and most of the work done requires the use of diffuse functions in the basis set (eg B3LYP/6-31+G(d,p)). Sometimes in these large systems I encounter situations where there is some near linear dependence and a resulting oscillation in the SCF with no converegence. I have tried all the standard tricks (vshift, xqc, changing the initial guess, nodiis, novaracc, starting from lower basis sets and computing force constants, etc) in Gaussian 03 Rev. e01 to resolve this. > > The only reliable fix I have found is to use IOp(3/59) (threshold for throwing away eigenvectors of S) and change it from the default 6 to some lower number, usually 5 (I can see that this results in an extra 10 or so [out of a 1000] basis sets being culled from the calculation). I was hoping someone could detail some of the consequences and possible pitfalls of changing the default value. > > Thanks, Ron> > From owner-chemistry@ccl.net Sun Jan 30 17:50:00 2011 From: "Jim Kress ccl_nospam]^[kressworks.com" To: CCL Subject: CCL: Symposia Message-Id: <-43800-110130155258-6433-v+EhYrnItyNRa4bBgdWFlg*server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 30 Jan 2011 15:52:30 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam||kressworks.com] Alejandro, Thank you for your excellent response. You understood the intent of my original posting, precisely. Webcasting, Webinars, and Podcasts represent an excellent alternative for those who cannot afford, or are unable, due to physical or geopolitical limitations, to travel to these symposia. They could also provide an excellent archival methodology for future use and/or distribution of the materials presented and discussed at these meetings. I can only encourage symposia organizers to investigate and provide this technology as a way to augment the accessibility, distribution and proliferation of their meetings across the planet. Especially to those of us who cannot afford to travel to every symposia we would wish to attend, > from which we would like to learn, and to which we would like to contribute. Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com ~~ ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com ~~ ccl.net] On Behalf Of Alejandro > Pisanty apisan+*+servidor.unam.mx > Sent: Saturday, January 29, 2011 2:21 AM > To: Kress, Jim > Subject: CCL: Symposia > > > Sent to CCL by: Alejandro Pisanty [apisan=-=servidor.unam.mx] > Hi, > > I will definitely side with Jim Kress on this one and expand. > > Herbert and Steen are not wrong in describing the importance of > networking > between people and ideas in face-to-face (f2f) conferences. > > But it is a false dilemma to oppose f2f interaction and online > interaction. > > The value of a streamed or recorded video of a talk in a conference can > be > of extreme value to a scientist or to students unable to travel to the > conference. > > And, more and more often, there is a continuum between the f2f and the > online relations. Online synchronous comment of speeches and talks > constitutes a healthy backchannel which may on occasion be even more > illuminating than the talk because of the open possibility of learning > of > the background, clarifying points on the go, etc. In many fields, a > webcast plus a vigourous tweetstream have become the norm (and I'm sure > a > number of CCL-related conferences are working that way; Jim's question > is > for the many which aren't.) > > This particular community, the CCL, is one of the strongest proofs of > the value we assign to "augmented" interactions which are not limited > to > the bursty nature of conference contact. We started being 100 people > (that > was the room's capacity) in a > meeting in Ohio. Jan Labanowski started an email discussion list in > 1991 > and we will now be 20 years into it. It is one of the healthiest > virtual > communities known. > > We as a profession are evolving, and sticking to face-to-face+email > seems > unnecessarily conservative. Let's wish/hope/ask that conference > organizers > do more to provide opportunities for remote interaction and let's all > expand the already vital online communication this list is known for. > > I would certainly welcome (on- or off-list) examples of > theoretical/quantum/computational chemistry events which have a strong > online or remote component and offer to provide examples from other, > related or exemplary fields. > > Yours, > > Alejandro Pisanty > > > . . . . . . . . . . . . . . . . . . . . . . . . > . . > Dr. Alejandro Pisanty > UNAM, Av. Universidad 3000, 04510 Mexico DF Mexico > > Tels. +52-(1)-55-5105-6044, +52-(1)-55-5418-3732 > > * Mi blog/My blog: http://pisanty.blogspot.com > * LinkedIn profile: http://www.linkedin.com/in/pisanty > * Twitter: http://twitter.com/apisanty > * Unete al grupo UNAM en LinkedIn, > http://www.linkedin.com/e/gis/22285/4A106C0C8614 > > * Ven a ISOC Mexico, http://www.isoc.org.mx, ISOC http://www.isoc.org > *Participa en ICANN, http://www.icann.org > . . . . . . . . . . . . . . . . . . . . . . . . > . . > > > On Fri, 28 Jan 2011, Herbert Fruchtl herbert.fruchtl:st-andrews.ac.uk > wrote: > > > Date: Fri, 28 Jan 2011 23:36:01 +0000 > > From: "Herbert Fruchtl herbert.fruchtl:st-andrews.ac.uk" > > > > Reply-To: CCL Subscribers > > To: "Pisanty, Alejandro " > > Subject: CCL: Symposia > > > > > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl#st-andrews.ac.uk] > >> > >> Is there any particular reason that none, or an insignificant > minority, of > >> these symposia are not being presented via webcast, webinars or > podcasts? > >> It would seem that those methods would make the symposia available > to a much > >> larger audience, providing for a much wider dissemination of > information, > >> while allowing for the acquisition of additional revenue for the > symposia > >> organizers and perhaps even lowering symposia costs. > >> > >> Is there any reason Corporations, Foundations, Universities, and > Government > >> Agencies are not adopting this 20th century technology for use in > the 21st? > >> > > The best technology to disseminate information or find out what's > going on in > > your field, in use for at least 3000 years, is to sit down with > people of > > similar interest over a beer and diss the boring session of talks you > just had > > to endure. > > > > Seriously: the "social" aspect of meeting people offline and face to > face, > > creating and refreshing collaborations and sometimes friendships, is > an aspect > > of conferences at least as important as the presentations themselves. > Following > > an online presentation is less useful than reading a paper. > > > > Herbert > > > > > > ------------------------------------------------------------------ > > University of St Andrews Webmail: https://webmail.st-andrews.ac.uk> To recover the email address of the author of the message, please > change> From owner-chemistry@ccl.net Sun Jan 30 23:56:01 2011 From: "Sumitro Harjanto sharjanto[*]i2r.a-star.edu.sg" To: CCL Subject: CCL: Calculating surface hydrophobicity Message-Id: <-43801-110130222804-22800-NWo+A2ARhyirWOxTdCANSg**server.ccl.net> X-Original-From: "Sumitro Harjanto" Date: Sun, 30 Jan 2011 22:28:02 -0500 Sent to CCL by: "Sumitro Harjanto" [sharjanto::i2r.a-star.edu.sg] Hi , I want to calculate the surface hydrophobicity of a protein molecule, but so far I only manage to use atomic partial charges as the estimate of the surface hydrophobicity, anyone can provide me some insight on how well is that as an estimate..? Also, it will be great help if anyone knows of any software/webtools/ that calculates surface hyrdrophobicity of protein, which generates some kind of grid output file. Thanks! (btw, my input file is in .pdb format) Cheers, Sumitro