From owner-chemistry@ccl.net Wed Jan 29 02:03:00 2014
From: "Stefan Grimme grimme^thch.uni-bonn.de" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL: Dispersion
Message-Id: <-49611-140129014856-4215-AeO2vSr+ub3ceDB5iqCc2Q(~)server.ccl.net>
X-Original-From: "Stefan  Grimme" <grimme _ thch.uni-bonn.de>
Date: Wed, 29 Jan 2014 01:48:55 -0500


Sent to CCL by: "Stefan  Grimme" [grimme:_:thch.uni-bonn.de]
Dear Cornie,
yes it is. The dispersion energy as an electron correlation effect has a short- and 
medium-range component which are not very well represented in approximate
standard GGAs and hybrids. This inter- or intramolecular component can 
change by sveral kcal/mol in a chemical reaction in particular for larger systems.
Over-repulsive functionals like e.g. B3LYP benefit most from dispersion
corrections. You might have a look to the following references for a more
detailed discussion:

WIREs Comput. Mol. Sci. (2011), 1, 211-228. DOI:10.1002/wcms.30
Phys. Chem. Chem. Phys. (2011), 13, 6670-6688. DOI:10.1039/c0cp02984j
ChemPhysChem (2011), 12, 1258-1261. DOI: 10.1002/cphc.201100127 DOI:10.1002/cphc.201100127
J. Org. Chem., (2012), 77, 10824-10834. DOI:10.1021/jo302156p

Any of the well tested corrections (D3, XDM, vdW-TS, VV10) or functionals
(M06* or more recent versions, double-hybrids) cure the problem.

Cheers!
Stefan


From owner-chemistry@ccl.net Wed Jan 29 03:40:00 2014
From: "Gert Kruger kruger]![ukzn.ac.za" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: Anouncement of new Molecular Modeling Journal
Message-Id: <-49612-140129024425-22740-j95lfIbFS+LJRzqeSP53bw=server.ccl.net>
X-Original-From: "Gert   Kruger" <kruger ~ ukzn.ac.za>
Date: Wed, 29 Jan 2014 02:44:24 -0500


Sent to CCL by: "Gert   Kruger" [kruger ~~ ukzn.ac.za]
Dear All,

Please take not of a relative new Journal - 
Journal of Organic and Biomolecular Simulations (Jobs).

Information about the journal can be found a http://thescipub.com/jobs.toc

Best wishes
Gert Kruger


From owner-chemistry@ccl.net Wed Jan 29 04:20:01 2014
From: "Jean-Pierre DJUKIC djukic*unistra.fr" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: Dispersion correction
Message-Id: <-49613-140129035837-16395-JrI6RUigVRAaLU7s7WzPxg * server.ccl.net>
X-Original-From: Jean-Pierre DJUKIC <djukic*|*unistra.fr>
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Date: Wed, 29 Jan 2014 09:58:29 +0100
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Sent to CCL by: Jean-Pierre DJUKIC [djukic:+:unistra.fr]


> Dear Cornie,
>
> Since the determination of a reaction profile depends on how well you
> determine substrate complex structures and transition states, the
> account of dispersion is crucial in tight and large systems wherein the
> nature of apparently innocent remote groups may well influence molecular
> arrangements and therefore affect the value of computed activation barriers. The
> best would be to compare two profiles, one drawn for geometries
> optimized with and  one for geometries optimized without dispersion.
> In some cases the difference is small. In some cases there is clearly no match.
Apart from dispersion,which is a recognized physical phenomenon, there 
are other issues associated with the computation of reaction profiles...
> Dispersion becomes key in large and extended systems like pointed out by
> Stefan Grimme.

>
>
> Good luck.
>
> JP


From owner-chemistry@ccl.net Wed Jan 29 09:35:00 2014
From: "=?ISO-8859-1?Q?Bj=F6rn_Sommer?= bjoern : CELLmicrocosmos.org" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: CELLmicrocosmos 2.2.2 MembraneEditor & VizBi 2014 Workshop Announcement
Message-Id: <-49614-140128215158-3207-AH778h4Z10FjPYlXBZQR2A-$-server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?Bj=F6rn_Sommer?= <bjoern]=[CELLmicrocosmos.org>
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Date: Wed, 29 Jan 2014 03:51:50 +0100
MIME-version: 1.0


Sent to CCL by: =?ISO-8859-1?Q?Bj=F6rn_Sommer?= [bjoern[#]CELLmicrocosmos.org]
Dear Colleagues,

the new major release of our


*CELLmicrocosmos 2.2.2 MembraneEditor*

is out now. This open source tool provides a 3D membrane modeling tool 
based on Java/Java WebStart for modeling PDB membranes based on Membrane 
Packing Algorithms. The shape-based visualization enables also the 
WYSIWYG modeling of larger membranes. The direct export to Jmol provides 
a fast preview of the molecular structures. Extended PDB properties 
enable the import of custom PDB files as well as the export to many 
different tools such as Gromacs. Different publications used the 
MembraneEditor already to model starting configurations for MD simulations.

But why talk a lot, if there are some videos on YouTube?

http://www.cellmicrocosmos.org/index.php/videos

The new release 2.2.2 comes now with a number of improvements:

- APL^Voro integration (optional on Linux and Mac OS X)
- The Wanderer Rookie for high-density membranes
- Extended capabilities of the Membrane Packing Algorithm interface
- Extended protocol capabilities
- Java 7 Update 51/Open JDK+Iced Tea compatibility
- Many bug fixes

More information, an extensive documentation, as well as the link to our 
J. Chem. Inf. Model. publication you will find here:

http://Cm2.CELLmicrocosmos.org


*VizBi Workshop Announcement - 3 days left!*

CELLmicrocomos Workshop: Molecular Modeling

If you or your students want to learn more about molecular modeling with 
the MembraneEditor, where to get data for compositions and how to use 
PDB membranes with external tools like Gromacs, you can attend our 
workshop at the VizBi in Heidelberg (04.03.2014). More information you 
will find here:

http://vizbi.org/2014/Program/#CELLmicrocosmos%20Workshop:%20Molecular%20Modeling

If you are interested, please register until end of January.


Happy Modeling!
Björn Sommer & team.CELLmicrocosmos.org


-- 

Björn Sommer
CELLmicrocosmos.org
Cell Modeling & Visualization
Bio-/Medical Informatics Group
Faculty of Technology
Bielefeld University
Germany
e-m bjoern^CELLmicrocosmos.org
h-p  www.CELLmicrocosmos.org


From owner-chemistry@ccl.net Wed Jan 29 11:08:00 2014
From: "Guegan Frederic frederic.guegan ~ ens-lyon.fr" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: Atomic spin values and directions in G09 =?UTF-8?Q?=3F?=
Message-Id: <-49615-140129095153-23602-cR15Ew3vlUy1Ij69p0eJug**server.ccl.net>
X-Original-From: Guegan Frederic <frederic.guegan : ens-lyon.fr>
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Date: Wed, 29 Jan 2014 15:51:44 +0100
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Sent to CCL by: Guegan Frederic [frederic.guegan*|*ens-lyon.fr]
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Dear CCLers,
I wondered if any of you knew a way to obtain the atomic magnetic
momentum out of a Gaussian (DFT, but also post-HF like DDCI) calculation
? I am indeed interested in the computation of the magnetic properties
of discrete coordination complexes, and I would like to know whether it
is possible to obtain not only a single point value like in the usual
condensation schemes (such as Mulliken) but also a direction, that is to
say to print an "atomic spin vector".
I already looked in the Gaussian technical supports, and found an IOP
that should have adressed this problem (4/127=1), but I did not get any
extra lines in my outputs (both .log and .fch) when using this
specification.
For you information, the corresponding input line : 

#p ub3lyp/lanl2dz iop(4/127=1)

Any help would be much appreciated! Kind regards,

FRÉDÉRIC GUÉGAN
Team Chemometry and Modelling (CHEMOD)
Institute for Analytical Sciences of Lyon (UMR CNRS/UCBL/ENS) -
VILLEURBANNE
http://modelisa.univ-lyon1.fr/guegan.html

 
--=_c78e8d7e4b31cb4fb576df157bf23c5d
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html; charset=UTF-8

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN">
<html><body style=3D'font-family: Verdana,Geneva,sans-serif'>
<p>Dear CCLers,<br />I wondered if any of you knew a way to obtain the atom=
ic magnetic momentum out of a Gaussian (DFT, but also post-HF like DDCI) ca=
lculation ? I am indeed interested in the computation of the magnetic prope=
rties of discrete coordination complexes, and I would like to know whether =
it is possible to obtain not only a single point value like in the usual co=
ndensation schemes (such as Mulliken) but also a direction, that is to say =
to print an "atomic spin vector".<br />I already looked in the Gaussian tec=
hnical supports, and found an IOP that should have adressed this problem (4=
/127=3D1), but I did not get any extra lines in my outputs (both .log and =
=2Efch) when using this specification.<br />For you information, the corres=
ponding input line : <br /><br />#p ub3lyp/lanl2dz iop(4/127=3D1)<br /><br =
/>Any help would be much appreciated! Kind regards,<br /><br /><br /><stron=
g><span style=3D"font-size: x-small;">Fr&eacute;d&eacute;ric Gu&eacute;gan<=
/span></strong><br /><span style=3D"font-size: x-small;">Team Chemometry an=
d Modelling (CHEMOD)</span><br /><span style=3D"font-size: x-small;">Instit=
ute for Analytical Sciences of Lyon (UMR CNRS/UCBL/ENS) - VILLEURBANNE</spa=
n><br /><span style=3D"font-size: x-small;">http://modelisa.univ-lyon1.fr/g=
uegan.html</span><br /><br /></p>
</body></html>

--=_c78e8d7e4b31cb4fb576df157bf23c5d--


From owner-chemistry@ccl.net Wed Jan 29 22:59:00 2014
From: "Radoslaw Kaminski rkaminski.rk]=[gmail.com" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: Open-shell TDDFT in ADF & transition density
Message-Id: <-49616-140129225745-2017-u/JqU7wOnvd/VKuOXwe3Bw^^^server.ccl.net>
X-Original-From: "Radoslaw  Kaminski" <rkaminski.rk\a/gmail.com>
Date: Wed, 29 Jan 2014 22:57:44 -0500


Sent to CCL by: "Radoslaw  Kaminski" [rkaminski.rk=-=gmail.com]
Dear All,

I performed a TDDFT computation on the open-shell molecule in ADF. Some of the most relevant keywords are listed below:

Relativistic Scalar ZORA
Symmetry NoSym
Unrestricted
Charge 0 4
ExactDensity
Excitations
  Lowest 100
End
Save TAPE21

The output file looks fine, all requested transitions were computed, the spectrum is nicely visualized with adfpectra program etc. I then used the TAPE21 file in the densf utility to produce transition densities with the keywords:

Density Fit Trans

However, the resultant TAPE41 file does not contain any information about the transition densities. Any other density or orbitals looks OK if computed with densf. Am I missing some additional keyword or something like that?

Thanks in advance,

Radek