From owner-chemistry@ccl.net Mon Apr 1 00:59:00 2013 From: "Ramesh Kumar Chitumalla rameshchitumalla%a%gmail.com" To: CCL Subject: CCL: MO's in Solvent Message-Id: <-48501-130401005642-3154-rDhf0IfVRLb4XwX3O7EESA.:.server.ccl.net> X-Original-From: "Ramesh Kumar Chitumalla" Date: Mon, 1 Apr 2013 00:56:41 -0400 Sent to CCL by: "Ramesh Kumar Chitumalla" [rameshchitumalla#%#gmail.com] Dear Prof. Andreas Klamt, Thank you very much for the detailed explanation and useful information. -Ramesh > "Andreas Klamt klamt,,cosmologic.de" wrote: > > Sent to CCL by: Andreas Klamt [klamt{=}cosmologic.de] > Since my first two attempts were not posted yet, here again my comment: > > Dear Ramesh, > > this is a good question. In the way as most continuum models are > implemented nowadays, the orbitals do not make much sense, because the > polarization charges are completely treated as external field, and the > energy for generatig the field is added to the total energy of the > molecule after the SCF has achieved. In my original COSMO implementation > in MOPAC I followed a different concept, considering the continuum > contribution as an indirect charge-charge interaction. In that way you > have additional nuclei-nuclei-interactions, additional > nuclei-electron-interactions (added to the one electron Hamiltonian, and > additional electron-electron interactions, added to the > two-electron-interactions. Thus the continuum interactions enter the > orbitals in a perfectly analogous way to the Coulomb interactions. A > post-correction for the self energy of the polarization field is not > required, since all energy contributions already take it into account by > the factor 1/2. While the total energy, and all expectation values will > be exactly the same in both implementations, the orbital energies > produced in that way are considerably different from thse in the > standard way, but I am convinced they make more sense. (Without > understand it in detail, Zerner and coworker had earlier called the > models as model A and B, see Szafran, et al. J. Comp. Chem 1993 ....) > > Please note the difference of the models for the orbitals: In the > standard implementation, the electrons in the LUMO "see" the > polarization charge polarization charges produced by the ground state > electron density, i.e. the change of the polarization charges due to the > excitation to the LUMO is missing. > > But I am afraid, currently no implementation of PCM or COSMO following > the Coulomb energy analogy is available. While writing this I realize > that I may be wrong: The GAMESS COSMO implementation may still have it. > Kim Baldridge should know about this best. > > Best regards > > Andreas > > From owner-chemistry@ccl.net Mon Apr 1 06:41:00 2013 From: "typ2469 typ2469]-[126.com" To: CCL Subject: CCL: how to select the parameters of EHMO, CNO, INDO, MINDO3, MNDO, AM1, PM3, etc for Hyperchem program Message-Id: <-48502-130331234419-8395-ZbkFe/8ZcJbPugo9kFNaLg|server.ccl.net> X-Original-From: typ2469 Content-Type: multipart/alternative; boundary="----=_Part_134236_885078918.1364787811033" Date: Mon, 1 Apr 2013 11:43:31 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: typ2469 [typ2469/./126.com] ------=_Part_134236_885078918.1364787811033 Content-Type: text/plain; charset=GBK Content-Transfer-Encoding: 7bit Hi, Could somebody tell me something about Hyperchem? For example, how to select the parameters of EHMO, CNO, INDO, MINDO3, MNDO, AM1, PM3, etc. What are the criterion and method for a set of approriate parameters for different molecules? Thank you . Best wishes Dr. Yi-Ping Tong ------=_Part_134236_885078918.1364787811033 Content-Type: text/html; charset=GBK Content-Transfer-Encoding: 7bit
Hi,
 
Could somebody tell me something about Hyperchem? For example, how to select the parameters of EHMO, CNO, INDO, MINDO3, MNDO, AM1, PM3, etc. What are the criterion and method for a set  of approriate parameters for different molecules? Thank you .
 
Best wishes
 
Dr. Yi-Ping Tong
 
 
 
 


------=_Part_134236_885078918.1364787811033-- From owner-chemistry@ccl.net Mon Apr 1 08:17:00 2013 From: "Ramesh Kumar Chitumalla rameshchitumalla ~ gmail.com" To: CCL Subject: CCL: MO's in Solvent Message-Id: <-48503-130401005953-3576-CyCsZSqo7KvyT5nC12+6BQ:+:server.ccl.net> X-Original-From: "Ramesh Kumar Chitumalla" Date: Mon, 1 Apr 2013 00:59:52 -0400 Sent to CCL by: "Ramesh Kumar Chitumalla" [rameshchitumalla-$-gmail.com] Dear Prof. N. Sekar, Thank you very much for your response. -CH. Ramesh Kumar > "Prof. Dr. N. Sekar nethi.sekar++gmail.com" wrote: > > Sent to CCL by: "Prof. Dr. N. Sekar" [nethi.sekar!^!gmail.com] > --047d7bd76ee219fdb004d92ef286 > Content-Type: text/plain; charset=ISO-8859-1 > > Yes. You will be able to see the distribution of electrons within the > molecule in the HOMO and LUMO and see whether it is different in the > solvent environment. > > > On Sat, Mar 30, 2013 at 9:36 PM, Ramesh Kumar Chitumalla rameshchitumalla.. > gmail.com wrote: > > > > > Sent to CCL by: "Ramesh Kumar Chitumalla" [rameshchitumalla[#]gmail.com] > > Dears CCL'Rs > > > > I would like to compare the behavior of a positively charged Ru(II) Dye in > > Vacuum and in solvent (DMF) (using G09 package) and for the same, DFT and > > TDDFT > > calculations have been carried out and I generated the MOs in Vacuum and in > > solvent (DMF). Kindly let me know does the generation of MOs in solvent > > meaningful ? > > > > Any help is greatly appreciated. > > > > Thank you.> > > > > > > > -- > Thanks and regards > > Prof. Dr. N. Sekar CCol FSDC > Head, Department of Dyestuff Technology > Co-ordinator, UGC-CAS and Professor in Tinctorial Chemistry > Institute of Chemical Technology (formerly UDCT) > Matunga, Mumbai-400019 > > Mob +91-9867958452 > n.sekar*_*ictmumbai.edu.in > > website: http://ictmumbai.edu.in/Fac_FacDetails.aspx?fidno=116 > > --047d7bd76ee219fdb004d92ef286 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > >
Yes. =A0You will be able to see the distribution of electr= > ons within the molecule in the HOMO and LUMO and see whether it is differen= > t in the solvent environment.


class=3D"gmail_quote"> > On Sat, Mar 30, 2013 at 9:36 PM, Ramesh Kumar Chitumalla rameshchitumalla..= > gmail.com < "mailto:owner-chemistry*_*ccl.net" target=3D"_blank">owner- chemistry*_*ccl.net<= > /a>> wrote:
>
x #ccc solid;padding-left:1ex">
> Sent to CCL by: "Ramesh Kumar Chitumalla" [rameshchitumalla[#] href=3D"http://gmail.com" target=3D"_blank">gmail.com]
> Dears CCL'Rs
>
> I would like to compare the behavior of a positively charged Ru(II) Dye in<= > br> > Vacuum and in solvent (DMF) (using G09 package) and for the same, DFT and T= > DDFT
> calculations have been carried out and I generated the MOs in Vacuum and in= >
> solvent (DMF). Kindly let me know does the generation of MOs in solvent
> meaningful ?
>
> Any help is greatly appreciated.
>
> Thank you.
>
>
>
> -=3D This is automatically added to each message by the mailing script =3D-= > >
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--
Thanks = > and regards

Prof. Dr. N. Sekar=A0=A0 CCol FSDC
Head, Department o= > f Dyestuff Technology
Co-ordinator, UGC-CAS and Professor in Tinc= > torial Chemistry
> Institute of Chemical Technology (formerly UDCT)
Matunga, Mumbai-400019<= > br>
Mob +91-9867958452
rget=3D"_blank">n.sekar*_*ictmumbai.edu.in
>
=A0
> >
> > --047d7bd76ee219fdb004d92ef286-- > > From owner-chemistry@ccl.net Mon Apr 1 13:50:00 2013 From: "Jean Jules Fifen julesfifen_+_gmail.com" To: CCL Subject: CCL: Odd Gaussian Error with coordinates Message-Id: <-48504-130401134905-15268-LhHtfAj2o+ys7OPcWSvjKQ^_^server.ccl.net> X-Original-From: Jean Jules Fifen Content-Type: multipart/alternative; boundary=e89a8f23440f2e308004d9503c5d Date: Mon, 1 Apr 2013 18:48:57 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules Fifen [julesfifen#%#gmail.com] --e89a8f23440f2e308004d9503c5d Content-Type: text/plain; charset=ISO-8859-1 Dear Bradley, You have at least two means to address the pointed matter. *opt=(cartesian) guess=read geom=allcheck* ... If this does not work, add the *nosymm* keyword. Note that the pointed problem often occurs when one is running optimization on a previous optimized geometry without reading saved guess orbitals and geometry. Hope this would help. Best regards, Jean Jules FIFEN, Department of Physics, Faculty of Science, University of Ngaoundere, Cameroon. On 31 March 2013 21:27, Bradley Welch bwelch5---slu.edu < owner-chemistry###ccl.net> wrote: > > Sent to CCL by: "Bradley Welch" [bwelch5|slu.edu] > Dear All, > > I'm doing a optimization on Ni(CN)4 2- and I've had no problems with a z- > matrix optimization. I've been attempting to do a cartesian optimization > and > I get the following error. > > Problem with coordinate system. Error termination via Lnk1e in > /usr/local/g09/l103.exe at Sun Mar 31 15:15:13 2013. Job cpu time: 0 days > 0 > hours 2 minutes 55.0 seconds. File lengths (MBytes): RWF= 26 Int= > 0 D2E= 0 Chk= 2 Scr= 1 > > > My input geometry is the following: > > -2 1 > 6 0.000000000 1.906633000 0.000000000 > 28 0.000000000 0.000000000 0.000000000 > 6 1.906633000 0.000000000 0.000000000 > 6 -1.906633000 0.000000000 0.000000000 > 6 0.000000000 -1.906633000 0.000000000 > 7 -3.073424000 0.000000000 0.000000000 > 7 0.000000000 3.073424000 0.000000000 > 7 3.073424000 0.000000000 0.000000000 > 7 0.000000000 -3.073424000 0.000000000 > > > > > I noticed that somehow it results in a geometry that results in everything > being crushed together: > > 6 0.000000000 -0.000022807 0.000000000 > 28 0.000000000 0.000000000 0.000000000 > 6 -0.000022807 0.000000000 0.000000000 > 6 0.000022807 0.000000000 0.000000000 > 6 0.000000000 0.000022807 0.000000000 > 7 -0.000031382 0.000000000 0.000000000 > 7 0.000000000 0.000031382 0.000000000 > 7 0.000031382 0.000000000 0.000000000 > 7 0.000000000 -0.000031382 0.000000000 > > > As I mentioned I have had success with optimizing the geometry via > z-matrix, > but I would like to do it with cartesian as well. Is my issue related to > anyway with my CN ligands being far away from the Nickel center? I'm using > a > 6-311+G* basis set for this optimization with B3LYP. Any help with this > issue > would be greatly appreciated.> > > -- *J. Jules Fifen.* --e89a8f23440f2e308004d9503c5d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Bradley,
You hav= e at least two means to address the pointed matter.
opt=3D(cartesian) guess=3Dread geom=3Dallcheck .= ..
If this does not work, add the nosymm keyword.
Note that the pointed problem often occurs when one is running optimiza= tion on a previous optimized geometry without reading saved guess orbitals = and geometry.
Hope this would help.

Best r= egards,
Jean Jules FIFEN,
Department of = Physics,
Faculty of Science,
University o= f Ngaoundere, Cameroon.



On 31 March 2013 21:27, Bradley Welch bwelch5---slu.edu <owner-chemistry###ccl.net> wro= te:

Sent to CCL by: "Bradley =A0 Welch" [bwelch5|slu.edu]
Dear All,

I'm doing a optimization on Ni(CN)4 2- and I've had no problems wit= h a z-
matrix optimization. I've been attempting to do a cartesian optimizatio= n and
I get the following error.

=A0Problem with coordinate system. Error termination via Lnk1e in
/usr/local/g09/l103.exe at Sun Mar 31 15:15:13 2013. Job cpu time: =A00 day= s =A00
hours =A02 minutes 55.0 seconds. File lengths (MBytes): =A0RWF=3D =A0 =A0 2= 6 Int=3D
0 D2E=3D =A0 =A0 =A00 Chk=3D =A0 =A0 =A02 Scr=3D =A0 =A0 =A01


My input geometry is the following:

-2 1
6 =A0 =A0 =A0 =A00.000000000 =A0 =A0 =A01.906633000 =A0 =A0 =A00.000000000<= br> 28 =A0 =A0 =A0 0.000000000 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000000000 6 =A0 =A0 =A0 =A01.906633000 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000000000<= br> 6 =A0 =A0 =A0 -1.906633000 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000000000 6 =A0 =A0 =A0 =A00.000000000 =A0 =A0 -1.906633000 =A0 =A0 =A00.000000000 7 =A0 =A0 =A0 -3.073424000 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000000000 7 =A0 =A0 =A0 =A00.000000000 =A0 =A0 =A03.073424000 =A0 =A0 =A00.000000000<= br> 7 =A0 =A0 =A0 =A03.073424000 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000000000<= br> 7 =A0 =A0 =A0 =A00.000000000 =A0 =A0 -3.073424000 =A0 =A0 =A00.000000000



I noticed that somehow it results in a geometry that results in everything<= br> being crushed together:

6 =A0 =A0 =A0 =A00.000000000 =A0 =A0 -0.000022807 =A0 =A0 =A00.000000000 28 =A0 =A0 =A0 0.000000000 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000000000 6 =A0 =A0 =A0 -0.000022807 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000000000 6 =A0 =A0 =A0 =A00.000022807 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000000000<= br> 6 =A0 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000022807 =A0 =A0 =A00.000000000<= br> 7 =A0 =A0 =A0 -0.000031382 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000000000 7 =A0 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000031382 =A0 =A0 =A00.000000000<= br> 7 =A0 =A0 =A0 =A00.000031382 =A0 =A0 =A00.000000000 =A0 =A0 =A00.000000000<= br> 7 =A0 =A0 =A0 =A00.000000000 =A0 =A0 -0.000031382 =A0 =A0 =A00.000000000

As I mentioned I have had success with optimizing the geometry via z-matrix= ,
but I would like to do it with cartesian as well. Is my issue related to anyway with my CN ligands being far away from the Nickel center? I'm us= ing a
6-311+G* basis set for this optimization with B3LYP. Any help with this iss= ue
would be greatly appreciated.



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--
J. Jules Fifen.
--e89a8f23440f2e308004d9503c5d-- From owner-chemistry@ccl.net Mon Apr 1 20:32:00 2013 From: "Devang Sachdev dsachdev^^^nvidia.com" To: CCL Subject: CCL: Webinar this week - Learn about GROMACS on GPUs from Dr. Erik Lindahl Message-Id: <-48505-130401203008-3739-S7SFPOIkbJSa/zVUc7rYZw[-]server.ccl.net> X-Original-From: "Devang Sachdev" Date: Mon, 1 Apr 2013 20:30:07 -0400 Sent to CCL by: "Devang Sachdev" [dsachdev-.-nvidia.com] Hi Folks We have over 400 people registered for this webinar already and I wanted send out a note to those who may have missed this from last week. Also a reminder to those who plan to attend that the webinar is on Thursday this week. Please join us to learn about running the first multi-node, multi-GPU-enabled release 4.6 of GROMACS on Kepler GPUs from Dr. Erik Lindahl, the project leader for this popular molecular dynamics package. GROMACS 4.6 allows you to run your models up to 3x faster on GPUs compared to CPUs. In this webinar you will learn about new GROMACS features and performance with latest NVIDIA Kepler K20 GPUs. Thursday, April 4, 2013 9:00 AM - 10:00 AM PDT Register: http://goo.gl/DjoCe Thanks Devang Sachdev Sr. Product Manager - NVIDIA www.linkedin.com/in/devangsachdev