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" <owner-chemistry#,#server.ccl.net>
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 <victor|-|fluor.quimica.uniovi.es>
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Date: Wed, 14 Jan 2015 09:35:12 +0100
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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. V�ctor Lua�a
--
. . "La suma de la mediocridad y de la creatividad es
/ `' \ constante: a m�s 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 tambi�n es peor
| |'`'`| | que lo malo, porque la mediocridad no es un grado, es una
\/`'`'`'\/ actitud"
===(((==)))==================================+=========================
! Dr.V�ctor Lua�a ! Mediocrity is worse than
! Departamento de Qu�mica F�sica y Anal�tica ! 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" <owner-chemistry],[server.ccl.net>
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 <Michael.Sluydts-,-UGent.be>
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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" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL:G: help with optimization
Message-Id: <-50902-150114062339-32202-pNs6EFR1Nlut+5kR8EOheA,+,server.ccl.net>
X-Original-From: Hemlata Agarwala <cclhemlata]*[gmail.com>
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Date: Wed, 14 Jan 2015 16:53:34 +0530
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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
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<div dir=3D"ltr">Hi everyone<div><br></div><div>I am not very well acquaint=
ed with DFT.</div><div>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?</div><div>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><div><br></div><=
div>I will appreciate the help of anyone on this</div><div><br></div><div>T=
hank you</div><div><br></div><div>Regards</div><div>Hemlata</div></div>
--047d7b10c7cf54be5f050c9af82a--
From owner-chemistry@ccl.net Wed Jan 14 10:44:01 2015
From: "Harald Lanig harald.lanig-,-fau.de" <owner-chemistry- -server.ccl.net>
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 <harald.lanig .. fau.de>
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Date: Wed, 14 Jan 2015 12:38:09 +0100
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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 Ume�, 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" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL:G: help with optimization
Message-Id: <-50904-150114113911-5092-QYxzBAvdcazTS5mLJ6xsaw!=!server.ccl.net>
X-Original-From: Mariusz Radon <mariusz.radon:_:gmail.com>
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Date: Wed, 14 Jan 2015 17:39:03 +0100
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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" <owner-chemistry!A!server.ccl.net>
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" <jaymax36-.-gmail.com>
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" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL:G: help with optimization
Message-Id: <-50906-150114124120-15795-Z//UrwvJVlBRyivDiIaWLw]~[server.ccl.net>
X-Original-From: "Tobias Kraemer" <t.kraemer-x-hw.ac.uk>
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" <owner-chemistry#%#server.ccl.net>
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" <vijay.gopal.c_-_gmail.com>
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" <owner-chemistry.:.server.ccl.net>
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 <victor|,|fluor.quimica.uniovi.es>
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Date: Thu, 15 Jan 2015 02:30:42 +0100
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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. V�ctor Lua�a
--
. . "La suma de la mediocridad y de la creatividad es
/ `' \ constante: a m�s 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 tambi�n es peor
| |'`'`| | que lo malo, porque la mediocridad no es un grado, es una
\/`'`'`'\/ actitud"
===(((==)))==================================+=========================
! Dr.V�ctor Lua�a ! Mediocrity is worse than
! Departamento de Qu�mica F�sica y Anal�tica ! 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)