From owner-chemistry@ccl.net Thu May 17 00:18:01 2007 From: "Makoto Yamashita makotoy[a]chembio.t.u-tokyo.ac.jp" To: CCL Subject: CCL:G: error message from gaussview on Windows Vista Message-Id: <-34290-070517001417-21322-/Ez8fiCFroF3y6zKhq+QPA===server.ccl.net> X-Original-From: "Makoto Yamashita" Date: Thu, 17 May 2007 00:14:13 -0400 Sent to CCL by: "Makoto Yamashita" [makotoy^chembio.t.u-tokyo.ac.jp] Hello Daria, Thank you for kind suggestion. I tried to run the program as administrator, but Vista said same answer. I would appreciate if you or others tell me another possibility. Thanks, Makoto Yamashita > Sent to CCL by: "Daria Khvostichenko" [dkhvosti(a)uiuc.edu] > Hello, > Try "Run as administrator": right-click on the .exe or the shortcut, > and this option will appear there. You can also change the program's properties > to make it always run as administrator. > Daria >> Sent to CCL by: "Makoto Yamashita" >> [makotoy]*[chembio.t.u-tokyo.ac.jp] >> Hello, >> Has anyone tried to use Gaussview on Windows Vista? >> After usual installation of it on my Vista PC, >> running the program made an error message as follows: >> "failed to establish a temp directory" >> (Gauusian 03W is installed in c:\G03W folder as usual and is working well) >> I would appreciate if anybody suggested to solve this problem. >> Thank you, >> Makoto Yamashita >> The University of Tokyo From owner-chemistry@ccl.net Thu May 17 06:33:00 2007 From: "Fernando Mota Valeri f.mota|*|ub.edu" To: CCL Subject: CCL: Orca 2.6.0 with OpenMPI Message-Id: <-34291-070517062446-6399-rjiNxuItwFaQHg4vf19zBA[A]server.ccl.net> X-Original-From: Fernando Mota Valeri Content-Transfer-Encoding: 8bit Content-type: text/plain; format=flowed; delsp=yes; charset=ISO-8859-1 Date: Thu, 17 May 2007 11:44:09 +0200 MIME-version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Fernando Mota Valeri [f.mota|ub.edu] Hi, I'm trying to use the 2.6.0 version of ORCA program in parallel using OpenMPI and it doesn't recognize all cpus, only sees one, but runs two process simultaneously doing the same. At this moment i use the version 2.5 Rev. 00 and it works perfectly. ¿Is there anyone that knows if I have to change anything in the configuration of OpenMPI for doing ORCA to work? Thanks in advance Fernando Mota Valeri (e.mail: f.mota*ub.edu) Dept. Química Física, Univ. de Barcelona Tel: 93 402 19 17 . Fax: 93 402 12 31. From owner-chemistry@ccl.net Thu May 17 08:16:00 2007 From: "Rajarshi Guha rguha---indiana.edu" To: CCL Subject: CCL: Toxicology calculations Message-Id: <-34292-070517003053-26633-qMwJjDW0/od1fuyGeQ68LA%a%server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 16 May 2007 12:07:17 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha!=!indiana.edu] On May 16, 2007, at 9:51 AM, Marco Neves marco.neves-*-icrm.cnr.it wrote: > > Sent to CCL by: "Marco Neves" [marco.neves**icrm.cnr.it] > Dear all, > > Concerning the "in-silico" estimation of toxic activities of > chemical compounds, I wonder whether there are some free programs? > In particular, I would be interested in carcinogenicity predicions, > script filters to identify reactive chemical groups, or some other > tools. > Thanks in advance, Depending on the problem, we have a some models which are accessible on the web (though since they are based on web services, you can have arbitrary clients). Some examples include Ames mutagenicity model - http://rguha.ath.cx/~rguha/cicc/rws/ames/ Cytotoxicity models (based on the Jurkat cell line) - http:// rguha.ath.cx/~rguha/cicc/rws/scripps Anti-cancer activity (based on the NCI DTP 60 cell lines) - http:// rguha.ath.cx/~rguha/cicc/ncidtp/dtp You can also consider ToxTree (http://ambit.acad.bg/toxTree/) which includes a variety of prediction schemes based on a decision tree model ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- How I wish I were what I was when I wished I were what I am. From owner-chemistry@ccl.net Thu May 17 12:35:00 2007 From: "David A. Case case*scripps.edu" To: CCL Subject: CCL:G: Gibbs energy with solvent effects Message-Id: <-34293-070517114201-21890-GEcRoDcxk3esp/mdQRMMMQ,+,server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 17 May 2007 08:41:50 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case^_^scripps.edu] On Wed, May 16, 2007, Luis M Simon wrote: > > If I do not misunderstood Andreas Klamt point (sorry if I am completelly > wrong), the problem is that in the numerical evaluation of the hessian > computational chemistry programs calculates first derivatives and energies > on "perturbed" geometries, and that the cavity generated by the solvation > model is perturbed aswell (as the cavity is generated from the geometry). > > I have experienced some problems whith frequency calculations on fully > converged structures (with a solven model) that shows small negative > eigenvalues in the hessian, and it makes sense to me that these problems may > arrise as a "numerical noise" in the hessian evaluation. But if thats true, > the problem is not the solvent model, but the neccesity of using numerical > methods for calculating second derivatives. What about codes (like G03) that > implements analytical second derivatives in calculations with a cavity > solvation model? Will then they be more reliable? I believe that Dr. Klamt was not talking about technical problems in constructing the Hessian, but rather about a parameterization problem: > Sent to CCL by: Andreas Klamt > > The vibrational contributions to solvation (at room temperature) are already > implicitly aken into account in almost all solvation methods. Stated in another way: most implicit solvent models have adjustable parameters that were chosen such that calculation on rigid molecules would give (as closely as the model allows) an estimate of the experimental solvation free energies. So, it would not generally be consistent to explicitly add in vibrational calculations on top of this. Plus (as also pointed out earlier) it is not clear that equilibrium solvation models would correctly account for fast vibrations. ...hope this helps...dave case From owner-chemistry@ccl.net Thu May 17 13:09:00 2007 From: "Andreas Klamt klamt|*|cosmologic.de" To: CCL Subject: CCL:G: Gibbs energy with solvent effects Message-Id: <-34294-070517013543-15413-/6cYOMm5bSU0RMb/7CwB/w!=!server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 17 May 2007 07:34:52 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt(a)cosmologic.de] Dear Simon, you are misunderstanding my points! The first point is: Since normal solvation models are parameterized on dG_solv, without taking into account changes in the frequencies, this part of the free energy change has already been implicitly parameterized into the models, most likely through the surface proportional "non-dielectric" contributions. So it is dangerous to put these contributions explicitly on top of such solvation calculations. The second point is: If you calculate the second derivatives of the energy including a solvation term, then you get the second derivative of this energy assuming full equilibrium between the solute and all parts of the polarizability of the solvent. But in polar solvents a large part of the polarizability (in water ~ 98%) arises from the reorientation of permanent dipoles. These are too slow to follow fast vibrations. Hence the second derivative in solvation has not such a clear relation to the frequencies of vibrations as we are used to have it in gas phase. You would have to take into account frequency dependent dielectric constants, ... a rather unsolved area. The limit of very fast excitation (or vibrations) can most likely be treated with the assumption that only the electronic polarizability follows the perturbation. See for example my paper A. Klamt: 'Calculation of UV/Vis-Spectra in Solution', J. Phys. Chem. 1996, 100, 3349 For vibrations the situation is even more questionable due to the almost continuum of frequencies, and due to the fact that the assumption of solvent neighbors which adiabatically follow the vibrations is questionable. There should be an inertia of the neighbors, but it is not there in solvation Hamiltonians. So, just forget about the frequencies in solution from second derivatives of a PCM or COSMO calculation. COSMO-RS (COSMOtherm) provides expressions for the free energy and enthalpy of molecules in almost arbitrary solvents and mixtures at variable temperature. It has been widely validated on chemical engeneering vapor-liquid equilibria, and thus probably it is the most thermodynamic solvation model, if not the only one, available. For details best see my book "COSMO-RS: From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design", Elsevier, 2005 Best regards Andreas Luis M Simon luissimonrubio-#-hotmail.com schrieb: > Sent to CCL by: "Luis M Simon" [luissimonrubio*hotmail.com] > If I do not misunderstood Andreas Klamt point (sorry if I am completelly wrong), the problem is that in the numerical evaluation of the hessian computational chemistry programs calculates first derivatives and energies on "perturbed" geometries, and that the cavity generated by the solvation model is perturbed aswell (as the cavity is generated from the geometry). > > I have experienced some problems whith frequency calculations on fully converged structures (with a solven model) that shows small negative eigenvalues in the hessian, and it makes sense to me that these problems may arrise as a "numerical noise" in the hessian evaluation. But if thats true, the problem is not the solvent model, but the neccesity of using numerical methods for calculating second derivatives. What about codes (like G03) that implements analytical second derivatives in calculations with a cavity solvation model? Will then they be more reliable? > > Regards: > > Luis Simon > > > > Sent to CCL by: Andreas Klamt [klamt(!)cosmologic.de] > Hi Albert, > > as I already posted a few times: The vibrational contributions to solvation (at room temperature) are already implicitly aken into account in almost all solvation methods. It does not make any sense to combine them with explicit frequency calculations in the solvent, especially since the latter raise the question whther fast vibrations can be treated by equilibrium solvation. > > If you are going for Gibbs energies at variable temperature probably my COSMO-RS method (COSMOtherm program) is the only way to go (not just the COSMO-RS keyword in Gaussian!). > > Best regards > > Andreas > > Albert Poater albertpo%%stark.udg.es schrieb: > Sent to CCL by: "Albert Poater" [albertpo:-:stark.udg.es] > > > Dear Gaussian users, > I have one doubt. Which are the possible methods to calculate the Gibbs > energy using geometries optimized in gas phase? The calculation of > frequencies, + PCM, using these geometry is the most correct one? Or > taking the value for the free energy included in the PCM calculation is > also valid? And correcting the gas phase Gibbs energy by the free energy of the PCM calculation minus the energy also in PCM? > Hoping your comments, > Albert> > > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt,cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu May 17 18:14:00 2007 From: "Cheri A McFerrin cmcfer1^^^lsu.edu" To: CCL Subject: CCL: NAMD question Message-Id: <-34295-070517173446-32605-aG3Y9N5jKyF1D8pdWlWCcQ[-]server.ccl.net> X-Original-From: "Cheri A McFerrin" Date: Thu, 17 May 2007 17:34:42 -0400 Sent to CCL by: "Cheri A McFerrin" [cmcfer1||lsu.edu] hi all, i am interested in running a NAMD simulation using o-ter-phenyl (2 phenyl rings attached to a benzene at its ortho positions) as this molecule goes through a glass-transition temperature when the temperature is gradually lowered. i would like to represent o-ter-phenyl as 3 points in space with a rigid bond distance between these points, each point has zero charge, and the angle between the 3 points is approx 72 degrees. does anyone know how to run a NAMD simulation when the bond distances and angles are constrained to constant values? thanks in advance. cheri mcferrin