From owner-chemistry@ccl.net Fri Nov 18 09:49:00 2005 From: "Mark Thompson mark-x-arguslab.com" To: CCL Subject: CCL: Tinker: harmonic torsion potential Message-Id: <-29996-051117234157-27676-TbIdelXdjdQLBtM800//Jg!^!server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 17 Nov 2005 20:41:47 -0800 MIME-Version: 1.0 Sent to CCL by: Mark Thompson [mark###arguslab.com] Hi Gustavo, One trick that I've used is to verify MM first derivatives is to write a numerical gradient routine to go along with analytical first derivative code. Then choose high symmetry cases (small test systems) centered on the origin and tricks like that to test that numerical and analytical gradients agree (when you choose increasingly smaller displacements). Rotating the test system to different coordinate planes will allow you to possibly isolate x,y,z components (depends on the specifics of the type of interaction). This will only tell you if your first derivatives are internally consistent and not if your actual energy term is correct. However, with clever choice of simple test systems, you can usually verify by hand whether the energy term is correct. One warning about using other codes to debug your own codes....no guarantee they are correct either! ....though I am sure Tinker is in good shape since so many people have used it. Hope this helps. Mark Thompson Gustavo A Mercier gamercier(_)yahoo.com wrote: >Sent to CCL by: "Gustavo A Mercier" [gamercier{=}yahoo.com] >Hi! > >I am debugging a program. It would help if I could do some molecular mechanics with a force field that included a harmonic term for the torsions instead of the more common fourier series. TINKER (from Ponder's lab) has many options to modify the potential, including one for harmonic improper torsions. Is there a way of specifying a "proper" torsion harmonic term? I've gone over the manual and this does not seem to be an option. > >Thanks for your help! >Gustavo A. Mercier, Jr, MD,PhD >gamercier{=}yahoo.com >gustavom{=}baylorhealth.edu > > ---------------------------- Mark Thompson mark+*+arguslab.com http://www.arguslab.com ---------------------------- From owner-chemistry@ccl.net Fri Nov 18 10:24:00 2005 From: "Cory Pye cpye[-]crux.smu.ca" To: CCL Subject: CCL:G: sto-ng basis sets Message-Id: <-29997-051118093505-9299-S/O4aV/kxcypXWqvg2+QMA[#]server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 18 Nov 2005 10:34:51 -0400 (AST) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye:-:crux.smu.ca] Hello, I would imagine that this was done for computational expedience. If you use something like Gram-Schmidt orthonormalization, then instead of having a monomial times a Slater, you would have to have a polynomial times a slater. In a molecular calculation, then, you would have to do a 4-centre integral of the product of four different polynomials times four different Slaters. Another reason may be that it is difficult if not impossible to reproduce the nodal characteristics of say a 6s orbital with a STO-3G basis set. The SCF will generally try to project out the overlap. The orbital coefficients of the ns orbital will generally have multiple "large" entries for the n-1 s, n-2 s basis functions. Incidentally, I have an honours student who is extending the STO-NG basis sets for the heavier elements. On Thu, 17 Nov 2005, Alexander Kollias ackollias###gmail.com wrote: > Sent to CCL by: "Alexander Kollias" [ackollias{}gmail.com] > Greetings, > When the STO-NG basis sets were created by either non-linear least-squares regression or similar minimization routines why were basis functions (BF) that were not orthogonal to one another not orthogonalized? I am not referring to Pople's work where the nS and nP BFs were fit to have the same exponential coefficients and therefore, reducing computational intensity. More precisely I am referring to instances where the nS, nP, etc. BFs were each separately fit with a linear combination of GTOs [for example see R.F. Stewart J. Chem. Phys. 52, 431 (1970)]. > For instance and for the sake of simplicty, consider only the 1S and 2S BFs, which have an overlap of sqrt(3)/2 (~88%). Would it not be better to construct a 2S BF that is orthogonal to the 1S BF, via Gram-Schmidt orthonormalization. Thereby fitting the orthonormal 2s with a linear combination of Gaussian basis functions instead of replicating the 1S BF the dominant 1s "character" found in the 2S BF? > regards, > Alex Kollias > > ackolias{=}gmail.com > LCT Paris 6 Jussieu > Paris France.> > > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye^-^crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Fri Nov 18 10:59:01 2005 From: "luis simon luissimonrubio:+:hotmail.com" To: CCL Subject: CCL:G: G98 solvent model error Message-Id: <-29998-051118053715-8424-IyQ5G8YICWJHSAT//cVxTw ~ server.ccl.net> X-Original-From: "luis simon" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 18 Nov 2005 11:36:44 +0100 MIME-Version: 1.0 Sent to CCL by: "luis simon" [luissimonrubio*hotmail.com] I also had the same problem!!!!! (I wonder if there is any problem arising > from PCM implementation that I have not still suffer). But it was difficult to solve... (in fact, it was impossible to solve for me for G98W binary). It is related with the size of your system. There is a limit in the number of tessera (vertices in a poligon-like surface that surrounds your mollecule) that can only be modified at compiling time. So if you have the source code of your program (you can allways get the source code of GAMESS for free) and you read the doccumentation, you will be able to solve your problem recompilling it and including somehow the new limits. It worked for me with GAMESS, but at this moment I can not remember what did I exactly to get it solved. I hope that someone else in the list may help you. Luis Simón. ----- Original Message ----- > From: "ramesh r ramesh_ass-.-yahoo.co.in" To: "Simón, Luis Manuel " Sent: Thursday, November 17, 2005 7:39 PM Subject: CCL:G: G98 solvent model error > Sent to CCL by: ramesh r [ramesh_ass(!)yahoo.co.in] > --0-663550313-1132243962=:99468 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Dear all, > i am getting following error when i run polarizable continumm model calculation using Gaussian98. > > "TESSERA: too many vertices in a tessera" > > Could anybody help me out, > thanks in advance, > sincerely, > ramesh > > > --------------------------------- > Enjoy this Diwali with Y! India Click here > --0-663550313-1132243962=:99468 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear all,
i am getting following error when i run polarizable continumm model calculation using Gaussian98.
 
"TESSERA: too many vertices in a tessera"
 
Could anybody help me out,
thanks in advance,
sincerely,
ramesh 

>

> Enjoy this Diwali with Y! India Click here > --0-663550313-1132243962=:99468--> > > > From owner-chemistry@ccl.net Fri Nov 18 13:28:00 2005 From: "Xu Wang xwang6 . uky.edu" To: CCL Subject: CCL: PES scan of biphenyl Message-Id: <-29999-051118112207-17178-U212J891jQQ4rfvMa3KbGQ#%#server.ccl.net> X-Original-From: "Xu Wang" Sent to CCL by: "Xu Wang" [xwang6.:.uky.edu] I have a question about the potential energy surface scan for biphenyl (C12H10) about the dihedral angle between the two phenyl rings. The purpose of this calculation is to find out the rotational barrier of two phenyl rings. However, it seems that instead of twisting the entire phenyl group, only a single carbon and hydrogen atom move as I do the scan. I know some researchers have done this kind of work before. I wonder if anyone of you knows how to work this out. PS, I was using Gaussview 3.09 to build up the input file. Thanks! From owner-chemistry@ccl.net Fri Nov 18 14:19:00 2005 From: "Konrad Hinsen khinsen::cea.fr" To: CCL Subject: CCL: Tinker: harmonic torsion potential Message-Id: <-30000-051118141443-2613-WHMdOwdiAMMuaDJQp+4Mzg[A]server.ccl.net> X-Original-From: "Konrad Hinsen" Sent to CCL by: "Konrad Hinsen" [khinsen*cea.fr] On 18.11.2005, at 16:10, Mark Thompson mark-x-arguslab.com wrote: > One trick that I've used is to verify MM first derivatives is to write a > numerical gradient routine to go along with analytical first derivative > code. Then choose high symmetry cases (small test systems) centered on > the origin and tricks like that to test that numerical and analytical Another useful tool is automatic derivatives, in particular for non-trivial energy terms, as they permit a simple inspection of intermediate values. For the Python users out there, I provide a nicely packaged potential energy derivative module in my ScientificPython package, which is available at http://dirac.cnrs-orleans.fr/ScientificPython/ An example code for that module is: from Scientific.Physics.Potential import PotentialWithGradients from Scientific.Geometry import Vector def _harmonic(k,r1,r2): dr = r2-r1 return k*dr*dr harmonic = PotentialWithGradients(_harmonic) energy, gradients = harmonic(1., Vector(0,3,1), Vector(1,2,0)) print energy, gradients This prints 3.0 [Vector(-2.0,2.0,2.0), Vector(2.0,-2.0,-2.0)] There is also a version for second derivatives. ScientificPython also has "raw" automatic derivatives of arbitrary order in Scientific.Functions.Derivatives. -- ------------------------------------------------------------------------------- Konrad Hinsen Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen*_*cea.fr ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Nov 18 16:24:00 2005 From: "Vincent Xianlong Wang xloongw]=[yahoo.com" To: CCL Subject: CCL: PES scan of biphenyl Message-Id: <-30001-051118153929-1217-YCv88VTjz2c3y7n2pwhYDA()server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 18 Nov 2005 11:39:19 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw!A!yahoo.com] Hi Xu, The PES has been calculated before. See, (1) Cacelli, I.; Prampolini, G. Torsional Barriers and Correlations between Dihedarls in p-Polyphenyls. J. Phys. Chem. A 2003, 107, 8665-8670. In order to scan the PES with respect to the internal rotation of the phenyl groups, you need to define the internal rotational coordinate properly. Best regards, Xianlong --- "Xu Wang xwang6 . uky.edu" wrote: > Sent to CCL by: "Xu Wang" [xwang6.:.uky.edu] > I have a question about the potential energy surface > scan for biphenyl (C12H10) about the dihedral angle > between the two phenyl rings. The purpose of this > calculation is to find out the rotational barrier of > two phenyl rings. However, it seems that instead of > twisting the entire phenyl group, only a single > carbon and hydrogen atom move as I do the scan. I > know some researchers have done this kind of work > before. I wonder if anyone of you knows how to work > this out. PS, I was using Gaussview 3.09 to build up > the input file. Thanks! > > > > -= This is automatically added to each message by > the mailing script =- > 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.> > E-mail to administrators: CHEMISTRY-REQUEST!^!ccl.net > or use> > Before posting check wait time for next message at: > http://www.ccl.net> > If your mail bounces from CCL with 5.7.1 error, > check:> > > > __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com