From owner-chemistry@ccl.net Wed Jan 14 03:59:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor.:.fluor.quimica.uniovi.es" To: CCL Subject: CCL: Transition state optimization of biomolecular system Message-Id: <-50900-150114035425-23959-xt2b6gGambsU7Ol4u7hnwQ#,#server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Wed, 14 Jan 2015 09:35:12 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor^-^fluor.quimica.uniovi.es] On Tue, Jan 13, 2015 at 11:17:40AM -0500, Werner Crous crous.werner ~ gmail.com wrote: > Sent to CCL by: "Werner Crous" [crous.werner#,#gmail.com] > I am trying to do a QM/MM transition state optimization in NWCHEM. I obtained > a negative eigenvalue in the Hessian for which I followed the eigenvector. I then > did a vibrational analysis that gave me 1 negative frequency. However, > projecting out the rotations and translations eliminated this frequency. The > frequency was -49.29 cm-1. Visualization showed that the negative frequency > corresponds to a rotation around the center of mass of the QM system > obviously involving the reaction coordinate as well. I am concerned that there > are no low frequencies as one would expect for translations and rotations. What > can be the cause of this and is the reason for this result the fact that the wrong > mode was followed? Thank you in anticipation. Werner, Some information about which is your system would help to make an educated guess but ... may it be an internal rotation? If your molecule has two clear parts that rotate around a common axis but one rotates leftwards and the other rightwards that would match the pieces of your puzzle. Regards, Dr. Víctor Luaña -- . . "La suma de la mediocridad y de la creatividad es / `' \ constante: a más de la una menos de la otra" /(o)(o)\ (Jorge Wasenberg, 2015) /`. \/ .'\ "mediocrity+creativity=constant" / '`'` \ (First Principle of thermodynamics,Universal version) | \'`'`/ | "Lo mediocre es peor que lo bueno, pero también es peor | |'`'`| | que lo malo, porque la mediocridad no es un grado, es una \/`'`'`'\/ actitud" ===(((==)))==================================+========================= ! Dr.Víctor Luaña ! Mediocrity is worse than ! Departamento de Química Física y Analítica ! good, but is also worse ! Universidad de Oviedo, 33006-Oviedo, Spain ! than bad, because ! e-mail: victor===fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Wed Jan 14 09:34:01 2015 From: "Michael Sluydts Michael.Sluydts^UGent.be" To: CCL Subject: CCL: How can I Do Raman & IR in VASP? Message-Id: <-50901-150114042100-15405-E4KLh9dbzytx+5RfeBYifw],[server.ccl.net> X-Original-From: Michael Sluydts Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 14 Jan 2015 10:25:23 +0100 MIME-Version: 1.0 Sent to CCL by: Michael Sluydts [Michael.Sluydts _ UGent.be] Hello, These spectra are obtained through post-processing of phonon and dielectric tensor calculations. Note that these can require much higher accuracy settings than typical calculations to converge (dense k-mesh). I believe phonon can calculate these properties directly, but it isn't free. Phonopy is a free equivalent, but I believe it does not have a full implementation for this. (see this old discussion http://sourceforge.net/p/phonopy/mailman/message/31624979/ ). They do refer to another tool for IR: IR intensities: http://homepage.univie.ac.at/david.karhanek/downloads.html And a quick search shows some tools available for Raman: Raman: perhaps https://github.com/raman-sc/VASP I think searching around on google and in archives of phonopy (and even CCL) may provide you with some additional suggestions as well. Best regards, Michael Shawkat M Islam sislam###swin.edu.au schreef op 13/01/2015 om 21:34: > Sent to CCL by: "Shawkat M Islam" [sislam[*]swin.edu.au] > Hi CCL users, > > I am new to VASP. I want to perform Raman & IR analysis using VASP? Can > anybody please let me know what changes should I have to make in the INCAR > file. Any INCAR file with those parameters is highly appreciated. > > Thanks friend. > Shawkat > Swinburne University, Australia. > sislam]^[swin.edu.au> > -- ir. Michael Sluydts Center for Molecular Modeling Ghent University Technologiepark 903 9052 Zwijnaarde, Belgium tel. +32 (0)9 264 66 19 https://molmod.ugent.be From owner-chemistry@ccl.net Wed Jan 14 10:09:01 2015 From: "Hemlata Agarwala cclhemlata..gmail.com" To: CCL Subject: CCL:G: help with optimization Message-Id: <-50902-150114062339-32202-pNs6EFR1Nlut+5kR8EOheA,+,server.ccl.net> X-Original-From: Hemlata Agarwala Content-Type: multipart/alternative; boundary=047d7b10c7cf54be5f050c9af82a Date: Wed, 14 Jan 2015 16:53:34 +0530 MIME-Version: 1.0 Sent to CCL by: Hemlata Agarwala [cclhemlata(a)gmail.com] --047d7b10c7cf54be5f050c9af82a Content-Type: text/plain; charset=UTF-8 Hi everyone I am not very well acquainted with DFT. I have optimized a molecule and done frequency calculations on it. I have obtained a single point geometry and there is no negative frequency. Also, the output file shows "Normal termination of Gaussian". Is this information enough to conclude that the single point geometry which I have obtained is the minimum energy of the molecule and that the molecule is stable in that geometry, or do I need to do some other calculation(s) to arrive to the conclusion? One point to mention is that, when I open the single point geometry in a graphical visualization software like chemcraft, it shows a bond missing between the metal and one of the donor atoms in the molecule. What does this imply? Is it something very serious to ponder upon or should I just ignore it? I will appreciate the help of anyone on this Thank you Regards Hemlata --047d7b10c7cf54be5f050c9af82a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi everyone

I am not very well acquaint= ed with DFT.
I have optimized a molecule and done frequency calcu= lations on it. I have obtained a single point geometry and there is no nega= tive frequency. Also, the output file shows "Normal termination of Gau= ssian". Is this information enough to conclude that the single point g= eometry which I have obtained is the minimum energy of the molecule and tha= t the molecule is stable in that geometry, or do I need to do some other ca= lculation(s) to arrive to the conclusion?
One point to mention is= that, when I open the single point geometry in a graphical visualization s= oftware like chemcraft, it shows a bond missing between the metal and one o= f the donor atoms in the molecule. What does this imply? Is it something ve= ry serious to ponder upon or should I just ignore it?

<= div>I will appreciate the help of anyone on this

T= hank you

Regards
Hemlata
--047d7b10c7cf54be5f050c9af82a-- From owner-chemistry@ccl.net Wed Jan 14 10:44:01 2015 From: "Harald Lanig harald.lanig-,-fau.de" To: CCL Subject: CCL: [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany Message-Id: <-50903-150114063839-637-nq+HtoafNJs8COnwPoHZuA- -server.ccl.net> X-Original-From: Harald Lanig Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-15; format=flowed Date: Wed, 14 Jan 2015 12:38:09 +0100 MIME-Version: 1.0 Sent to CCL by: Harald Lanig [harald.lanig=-=fau.de] Dear list subscribers, I am very happy to announce that also this year, the traditional Molecular Modelling Workshop in Erlangen takes place on March, Monday 9th to Wednesday 11th, 2015. Starting on Monday after lunch should allow to avoid travelling on weekend keeping the expenses at a minimum. This time, the scientific program of the meeting is conducted by Dr. Bernd Beck, Boehringer-Ingelheim, Biberach, Germany. As usual, the workshop is organised by the german Section of the Molecular Graphics and Modelling Society. ####### Plenary Speakers ####### Over the last few decades computational chemistry, molecular modelling, and chemoinformatics became more and more an integral part of research in various areas of the chemical industry and at universities. A lot of new tools and new approaches together with a huge increase in computer power facilitates this development. Nevertheless there are still research topics where currently no or only limited support by in-silico methods is possible. We are very pleased to announce Prof. Anna Linusson University of Umeå, Sweden and Dr. Karl-Heinz Baringhaus Sanofi-Aventis Deutschland GmbH, Frankfurt/Main, Germany to discuss some of these topics from an academic and an pharmaceutical industry point of view. ####### Poster and Lecture Awards ####### As in the past years, there will be two poster awards of EUR 100 each and three lecture awards for the best oral presentations: 1st Winner: Travel bursary to attend the Young Modeller's Forum in London, UK, plus a speaker slot option at YMF (travel expenses are reimbursed up to EUR 500) 2nd Winner: EUR 200 travel expenses reimbursement 3rd Winner: EUR 100 travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. ####### Registration ####### As every year, an interesting and successful workshop depends on your contributions! Therefore let me invite you to submit talks and/or poster titles via the registration form accessible on the workshop website http://mmws2015.mgms-ds.de/index.php?m=register This website will provide all necessary information about the meeting! The deadline for all submissions is February 13th, 2015. We are looking forward to meeting you in Erlangen soon! -Bernd Beck Scientific Committe Workshop Organisation 2015 -Harald Lanig Chairman of the MGMS-DS e.V. -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen Fon +49 9131-85 20781 harald.lanig#%#fau.de Fax +49 9131-85 20785 http://www.zisc.uni-erlangen.de ------------------------------------------------------------------------ From owner-chemistry@ccl.net Wed Jan 14 11:49:01 2015 From: "Mariusz Radon mariusz.radon^_^gmail.com" To: CCL Subject: CCL:G: help with optimization Message-Id: <-50904-150114113911-5092-QYxzBAvdcazTS5mLJ6xsaw!=!server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 14 Jan 2015 17:39:03 +0100 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon,+,gmail.com] On 01/14/2015 12:23 PM, Hemlata Agarwala cclhemlata..gmail.com wrote: > Hi everyone > > I am not very well acquainted with DFT. > I have optimized a molecule and done frequency calculations on it. I > have obtained a single point geometry and there is no negative > frequency. Also, the output file shows "Normal termination of Gaussian". > Is this information enough to conclude that the single point geometry > which I have obtained is the minimum energy of the molecule and that the > molecule is stable in that geometry, or do I need to do some other > calculation(s) to arrive to the conclusion? Dear Hemlata, first of all, a little correction on terminology: the term "single point" [calculations] is used when you calculate an energy for a fixed structure (i.e., w/o optimization). But if you optimized the geometry you should call it "the optimized geometry," not "single point geometry." When you optimized the geometry and there is no negative frequency, it means that your structure corresponds to a local minimum on the potential energy surface. In this sense you, indeed, obtained a stable structure (i.e., not a transition state). However, it does not mean that your _local_ minimum is the _global_ minimum. Your molecule may have other energy minima (other conformers). To be sure what is the global minimum, you need to calculate the other conformations explicitly. This is, in general, very difficult and time consuming. So, think if your system may have some conformational diversity. Clearly, your result also does not mean that your molecule is "stable" in the usual chemical sense: it may be very reactive (for instance with solvent) and thus "unstable" from an experimental point of view. But this is probably too obvious to discuss... > One point to mention is that, when I open the single point geometry in a > graphical visualization software like chemcraft, it shows a bond missing > between the metal and one of the donor atoms in the molecule. What does > this imply? Is it something very serious to ponder upon or should I just > ignore it? > This implies that the bond length is too large compared with the sum of VdW radii (or other atomic radii), which are used by your program to make decision whether to draw a bond or not. That a bond is not drawn happens quite often for TM complexes, and there is nothing to worry about. You should look at the bond distance between the atoms, even if the bond is not drawn graphically. Take care, Mariusz -- Dr Mariusz Radon, Ph.D. Coordination Chemistry Group Faculty of Chemistry Jagiellonian University ul. Ingardena 3, 30-060 Krakow, Poland http://www2.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Wed Jan 14 14:48:01 2015 From: "Joseph Maxwell jaymax36-,-gmail.com" To: CCL Subject: CCL: Computational Chem. Code Snippets/Library Message-Id: <-50905-150114143658-24215-AIwzPg531ro+fQfej27yzA!A!server.ccl.net> X-Original-From: "Joseph Maxwell" Date: Wed, 14 Jan 2015 14:36:57 -0500 Sent to CCL by: "Joseph Maxwell" [jaymax36**gmail.com] Hello, Are there any general repositories of open source code snippets or library suitable for use in code generation in subroutines etc. Fortran, C, C++ PY are typical, but not necessarily, the only target. Thanks From owner-chemistry@ccl.net Wed Jan 14 15:26:01 2015 From: "Tobias Kraemer t.kraemer*hw.ac.uk" To: CCL Subject: CCL:G: help with optimization Message-Id: <-50906-150114124120-15795-Z//UrwvJVlBRyivDiIaWLw]~[server.ccl.net> X-Original-From: "Tobias Kraemer" Date: Wed, 14 Jan 2015 12:41:16 -0500 Sent to CCL by: "Tobias Kraemer" [t.kraemer**hw.ac.uk] Hi Hemlata, in response to your questions, here are a few points: (1) The absence of any imaginary modes from your frequency calculation confirms that the stationary point you have optimised to is indeed a minimum, as opposed to a saddle point of some order (such as a transition state). Now, whether or not this is the most stable geometry or not, depends somewhat on the complexity of the system. There are all sorts of problems associated with finding the most stable geometry, and this can be a challenging task. For example, there may be a large number of conformers that the molecule may adopt, or different spin states if a transition metal is present, for example. If you are looking at a relatively small and 'simple' molecule (i.e. you are sampling a rather small conformational space), say methane or benzene, than you can be relatively certain that the geometry optimisation has given you the lowest energy structure on the potential energy surface of that molecule. You could compare the structure to experimental data, say single crystal X-ray data, which would give you an idea how good your calculation was (it is another question how fair such a comparison to crystal structures is...). Regarding the stability of that molecule, it is not necessarily right to conclude from the pure existence of an optimized gas phase structure (!) that a molecule is also stable in a chemical sense. The term generally refers to thermodynamic stability. It's probably better to talk about relative stability here anyways. (2) The string "Normal Termination" at the end of the output tells you that Gaussian has indeed finished without an error. (3) The fact that your visualisation software doesn't draw a line to indicate the presence of a bond between two atoms should not worry you, in principle. The program uses a build-in list of threshold bond distances for which a line will be drawn, in fact this is much the same for any other visualisation software. So, any value smaller than the one in the database will result in a line being drawn (and accordingly you may get different line strength or layout for double or triple or hydrogen bonds). In fact, these values can be updated manually, so next time the program would draw a bond according to the new value in its list. Hope this helps to further shed some light on this. Best Tobi Dr. Tobias Kraemer Research Associate Institute of Chemical Sciences School of Engineering & Physical Sciences Heriot-Watt University Edinburgh EH14 4AS United Kingdom email: t.kraemer- -hw.ac.uk phone: +44 (0)131 451 3259 Hi everyone I am not very well acquainted with DFT. I have optimized a molecule and done frequency calculations on it. I have obtained a single point geometry and there is no negative frequency. Also, the output file shows "Normal termination of Gaussian". Is this information enough to conclude that the single point geometry which I have obtained is the minimum energy of the molecule and that the molecule is stable in that geometry, or do I need to do some other calculation(s) to arrive to the conclusion? One point to mention is that, when I open the single point geometry in a graphical visualization software like chemcraft, it shows a bond missing between the metal and one of the donor atoms in the molecule. What does this imply? Is it something very serious to ponder upon or should I just ignore it? I will appreciate the help of anyone on this Thank you Regards Hemlata From owner-chemistry@ccl.net Wed Jan 14 16:01:01 2015 From: "vijay CHILKURI vijay.gopal.c!A!gmail.com" To: CCL Subject: CCL:G: gaussian basis set less charged Pseudopotentials Message-Id: <-50907-150114135215-20971-y85jtW8BuKrpqiQ2NGqXtg#%#server.ccl.net> X-Original-From: "vijay CHILKURI" Date: Wed, 14 Jan 2015 13:52:04 -0500 Sent to CCL by: "vijay CHILKURI" [vijay.gopal.c^^^gmail.com] Hi, I solicit the aid of the aid of the CCL community in exchange for *Internet Karma* ! I would like to know if one could use Pseudopotentials (in gaussian G09) for metals/anions which are not only for core electrons. In other words, i want to know if it is possible to use Pseudopotentials (in G09) for the whole atom without any basis sets and a charge (+ for metal - for anion). For e.g. in Molcas Ca can be used as a Pseudopotential with charge +2 without any basis set, like so: /Ca.ECP.Pascual.0s.0s.0e-AIMP-CaO. J.L.Pascual, L.Seijo, Z.Barandiaran, J.Chem.Phys. 98(1993)9715. In case this is not possible, how would one try and represent a metal and it's surrounding ligand anions without any basis sets and at the same time prevent electrons from approaching it. Does something similar to the "electron repulsive term" exist for point charges in G09 ? thanks a lot, vijay From owner-chemistry@ccl.net Wed Jan 14 20:52:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor=fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: gaussian basis set less charged Pseudopotentials Message-Id: <-50908-150114205001-29122-fjDmGjwIwIqwH0UKaeFDTg.:.server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Thu, 15 Jan 2015 02:30:42 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor+/-fluor.quimica.uniovi.es] On Wed, Jan 14, 2015 at 01:52:04PM -0500, vijay CHILKURI vijay.gopal.c!A!gmail.com wrote: > > Sent to CCL by: "vijay CHILKURI" [vijay.gopal.c^^^gmail.com] > I would like to know if one could use Pseudopotentials (in gaussian G09) for > metals/anions which are not only for core electrons. > > In other words, i want to know if it is possible to use Pseudopotentials (in > G09) for the whole atom without any basis sets and a charge (+ for metal - for > anion). We did many years ago using an older version of gaussian and a more primitive embedding technique but similar to what you are asking for: Phys Rev B 64 (2001) 104102-1--11 I'll try to recover the scripts I did for that kind of modelling. Maybe you can adapt them to the g09 version. Regards, Dr. Víctor Luaña -- . . "La suma de la mediocridad y de la creatividad es / `' \ constante: a más de la una menos de la otra" /(o)(o)\ (Jorge Wasenberg, 2015) /`. \/ .'\ "mediocrity+creativity=constant" / '`'` \ (First Principle of thermodynamics,Universal version) | \'`'`/ | "Lo mediocre es peor que lo bueno, pero también es peor | |'`'`| | que lo malo, porque la mediocridad no es un grado, es una \/`'`'`'\/ actitud" ===(((==)))==================================+========================= ! Dr.Víctor Luaña ! Mediocrity is worse than ! Departamento de Química Física y Analítica ! good, but is also worse ! Universidad de Oviedo, 33006-Oviedo, Spain ! than bad, because ! e-mail: victor{}fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)