From owner-chemistry@ccl.net Tue Jul 19 08:36:00 2011 From: "Tristan Youngs t.youngs[-]qub.ac.uk" To: CCL Subject: CCL: Aten v1.7 Released. Message-Id: <-45105-110719083516-25247-YwbSwoNz+p7tZK2GBp8YPw-*-server.ccl.net> X-Original-From: "Tristan Youngs" Date: Tue, 19 Jul 2011 08:35:13 -0400 Sent to CCL by: "Tristan Youngs" [t.youngs+/-qub.ac.uk] Dear CCL, The latest version of Aten (v1.7) is now ready for download (Linux, Mac, and Windows) at www.projectaten.net. This release addresses (as usual) many bugs and adds many improvements, not least of which are: o A redesigned and better GUI o Improved renderer, including display of multiple models at once o Completely new Disorder Builder Wizard, able to create multiple-component systems of specific size, density, and population on demand o A fully reformatted and enhanced PDF manual o Better control over model export options when saving from the command-line or in batch mode o Fixes to spacegroup packing o Updates to old filters (including GAMESS-US) and addition of EPSR ATO file filter o Configurable saving of trajectory / vibration movies (using, for instance, mencoder) o Direct energy minimisation of systems using MOPAC (if installed) As always, feedback is welcome. Cheers, Tris. From owner-chemistry@ccl.net Tue Jul 19 10:58:00 2011 From: "Daniel Jana dfjana-*-gmail.com" To: CCL Subject: CCL:G: molecular geometry visualization on GaussView Message-Id: <-45106-110719105451-26085-8q6PEwwI/YYSVc51x9NtTQ ~~ server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 19 Jul 2011 16:54:42 +0200 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana[#]gmail.com] Hello, What you describe in 1) is most likely a problem you find at the last digit of the numbers and should be caused while rounding off numbers at printing time. At whatever level of computation you were doing (except perhaps CCSDTQ with some 7-tuple-zeta basis set) simply changing the basis set (or the functional, should you be using DFT) is going to affect the geometry more than what you see there. No method is that accurate, so worrying about the 10^-7 A digit is (mostly) pointless. Regarding your question number 2 I have no idea, I never use GaussView. From other programs I know it seems to be distance based... Best, Daniel On 17 July 2011 06:09, Hyunbok Lee mutebeat*gmail.com wrote: > > Sent to CCL by: "Hyunbok  Lee" [mutebeat/./gmail.com] > Dear all, > > I performed geometry optimization of a molecule with Gaussian 09. > > The output was visualized by GaussView 5.0 and I have two questions about it. > > > 1. Cartesian coordinates varied with output file type, *.out or *.chk. > Although the differences are very small, (~10^-7 A orders) > it is possible? I think that they must have the exactly same geometry > because both 'out' and 'chk' come from the same calculation. > (An error was not found in my out file.) > > > 2. How are 'bonds' determined in molecular geometry visualization on GaussView? > Atomic bonds in the molecule were also not the same due to the above reason. > What is the parameter whether two atoms bond or not? (atomic distance?) > And can I modify the bond when I load 'chk' file? > > > Thanks in advance. > > Hyunbok Lee>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Tue Jul 19 15:03:00 2011 From: "Neranjan Perera neranjan007+/-gmail.com" To: CCL Subject: CCL: software to optimize a large molecule Message-Id: <-45107-110719150205-17376-Nd2edlBP1n3X3QyUKPqU4g++server.ccl.net> X-Original-From: "Neranjan Perera" Date: Tue, 19 Jul 2011 15:02:02 -0400 Sent to CCL by: "Neranjan Perera" [neranjan007#gmail.com] Hi CCL users, I have a task of optimizing a molecule, which has close to 350 atoms, including metal atoms. I have found following softwares which in my view will do a good job. While searching I have unidentified the following as viable softwares; abinit siesta quantum espresso . I have started my calculations using abinit, but by the looks of it , as the system is large it will take quite a time to optimize. I do like to know your input on this matter. You might have much more experience in handling these softwares and would like to know from above which can be considered a better choice? Thank you very much for your input and it's highly appreciated. Neranjan From owner-chemistry@ccl.net Tue Jul 19 16:47:00 2011 From: "Arne Dieckmann adieckma%a%googlemail.com" To: CCL Subject: CCL: software to optimize a large molecule Message-Id: <-45108-110719162920-14078-lpniXhCdMNwtUyzmWHAH3g _ server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 19 Jul 2011 22:29:01 +0200 Mime-Version: 1.0 (iPhone Mail 8J2) Sent to CCL by: Arne Dieckmann [adieckma[]googlemail.com] It depends on the level of theory you would like to apply. What would that be? DFT? Arne On Jul 19, 2011, at 21:02, "Neranjan Perera neranjan007+/-gmail.com" wrote: > > Sent to CCL by: "Neranjan Perera" [neranjan007#gmail.com] > Hi CCL users, > I have a task of optimizing a molecule, which has close to 350 atoms, including metal atoms. I have found following softwares which in my view will do a good job. While searching I have unidentified the following as viable softwares; > abinit > siesta > quantum espresso . > > I have started my calculations using abinit, but by the looks of it , as the system is large it will take quite a time to optimize. I do like to know your input on this matter. You might have much more experience in handling these softwares and would like to know from above which can be considered a better choice? > > Thank you very much for your input and it's highly appreciated. > > Neranjan> > From owner-chemistry@ccl.net Tue Jul 19 18:07:00 2011 From: "neranjan perera neranjan007^gmail.com" To: CCL Subject: CCL: software to optimize a large molecule Message-Id: <-45109-110719174559-24574-A66yDsMjOIy3+3674TvTkA .. server.ccl.net> X-Original-From: neranjan perera Content-Type: multipart/alternative; boundary=000325554c86ede97204a8730965 Date: Tue, 19 Jul 2011 17:45:48 -0400 MIME-Version: 1.0 Sent to CCL by: neranjan perera [neranjan007[*]gmail.com] --000325554c86ede97204a8730965 Content-Type: text/plain; charset=ISO-8859-1 Yes, it's DFT that I would like to apply On Tue, Jul 19, 2011 at 4:29 PM, Arne Dieckmann adieckma%a%googlemail.com < owner-chemistry(-)ccl.net> wrote: > > Sent to CCL by: Arne Dieckmann [adieckma[]googlemail.com] > It depends on the level of theory you would like to apply. What would that > be? DFT? > > Arne > > On Jul 19, 2011, at 21:02, "Neranjan Perera neranjan007+/-gmail.com" > wrote: > > > > > Sent to CCL by: "Neranjan Perera" [neranjan007#gmail.com] > > Hi CCL users, > > I have a task of optimizing a molecule, which has close to 350 atoms, > including metal atoms. I have found following softwares which in my view > will do a good job. While searching I have unidentified the following as > viable softwares; > > abinit > > siesta > > quantum espresso . > > > > I have started my calculations using abinit, but by the looks of it , as > the system is large it will take quite a time to optimize. I do like to know > your input on this matter. You might have much more experience in handling > these softwares and would like to know from above which can be considered a > better choice? > > > > Thank you very much for your input and it's highly appreciated. > > > > Neranjan> > > -- Neranjan Perera Graduate Student Department of Chemistry University of Connecticut 55 North Eagleville Road Unit 3060 storrs, CT 06269 --000325554c86ede97204a8730965 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Yes, it's DFT that I would like to apply



On Tue, Jul 19, 2011 at 4:29 PM, Arne Dieckmann adieckma%a%googlemail.com <owner-chemistry(-)ccl.net> wrote:

Sent to CCL by: Arne Dieckmann [adieckma[]googlemail.com]
It depends on the level of theory you would like to apply. What would that = be? DFT?

Arne

On Jul 19, 2011, at 21:02, "Neranjan Perera neranjan007+/-gmail.com" <owner-chemistry_= ._ccl.net> wrote:

>
> Sent to CCL by: "Neranjan =A0Perera" [neranjan007#gmail.com]
> Hi CCL users,
> =A0 I have a task of optimizing a molecule, which has close to 350 ato= ms, including metal atoms. I have found following softwares which in my vie= w will do a good job. While searching I have unidentified the following as = viable softwares;
> abinit
> siesta
> quantum espresso =A0.
>
> I have started my calculations using abinit, but by the looks of it , = as the system is large it will take quite a time to optimize. I do like to = know your input on this matter. You might have much more experience in hand= ling these softwares and would like to know from above which can be conside= red a better choice?
>
> Thank you very much for your input and it's highly appreciated. >
> Neranjan>
>



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Neranj= an Perera
Graduate Student
Department of Chemistry
University of Connectic= ut
55 North Eagleville Road
Unit 3060
storrs, CT 06269
--000325554c86ede97204a8730965-- From owner-chemistry@ccl.net Tue Jul 19 21:51:00 2011 From: "Esteban Gabriel Vega Hissi egvega*gmail.com" To: CCL Subject: CCL: software to optimize a large molecule Message-Id: <-45110-110719191818-12281-R1CsKOF+OEeWbDuDFb9dag]-[server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=90e6ba53a4a850963f04a87454a6 Date: Tue, 19 Jul 2011 20:17:51 -0300 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega__gmail.com] --90e6ba53a4a850963f04a87454a6 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, You could try MOPAC2009 with PM6 level of theory! Hope this help! On Tue, Jul 19, 2011 at 6:45 PM, neranjan perera neranjan007^gmail.com < owner-chemistry,ccl.net> wrote: > Yes, it's DFT that I would like to apply > > > > On Tue, Jul 19, 2011 at 4:29 PM, Arne Dieckmann adieckma%a%googlemail.com > wrote: > >> >> Sent to CCL by: Arne Dieckmann [adieckma[]googlemail.com] >> It depends on the level of theory you would like to apply. What would th= at >> be? DFT? >> >> Arne >> >> On Jul 19, 2011, at 21:02, "Neranjan Perera neranjan007+/-gmail.com" >> wrote: >> >> > >> > Sent to CCL by: "Neranjan Perera" [neranjan007#gmail.com] >> > Hi CCL users, >> > I have a task of optimizing a molecule, which has close to 350 atoms= , >> including metal atoms. I have found following softwares which in my view >> will do a good job. While searching I have unidentified the following as >> viable softwares; >> > abinit >> > siesta >> > quantum espresso . >> > >> > I have started my calculations using abinit, but by the looks of it , = as >> the system is large it will take quite a time to optimize. I do like to = know >> your input on this matter. You might have much more experience in handli= ng >> these softwares and would like to know from above which can be considere= d a >> better choice? >> > >> > Thank you very much for your input and it's highly appreciated. >> > >> > Neranjan> >> > >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D-** >> E-mail to subscribers: CHEMISTRY++ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST++ccl.net or use>> **>> >> >> > > > -- > Neranjan Perera > Graduate Student > Department of Chemistry > University of Connecticut > 55 North Eagleville Road > Unit 3060 > storrs, CT 06269 > > --=20 Esteban Gabriel Vega Hissi =C1rea de Qu=EDmica F=EDsica Departamento de Qu=EDmica Universidad Nacional de San Luis Argentina --90e6ba53a4a850963f04a87454a6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

You could try MOPAC2009 with PM6 level of theory!

Hope th= is help!

On Tue, Jul 19, 2011 at 6:45 PM,= neranjan perera neranjan007^gmail.com <owner-chemist= ry,ccl.net> wrote:
Yes, it's DFT= that I would like to apply



On Tue, Jul 19, 2011 at 4:29 PM, Arne Dieckmann adieckma%a%googlemail.com &l= t;owner-chemi= stry++ccl.net> wrote:

Sent to CCL by: Arne Dieckmann [adieckma[]googlemail.com]
It depends on the level of theory you would like to apply. What would that = be? DFT?

Arne

On Jul 19, 2011, at 21:02, "Neranjan Perera neranjan007+/-gmail.com" <owner-chemistry_= ._ccl.net> wrote:

>
> Sent to CCL by: "Neranjan =A0Perera" [neranjan007#gmail.com]
> Hi CCL users,
> =A0 I have a task of optimizing a molecule, which has close to 350 ato= ms, including metal atoms. I have found following softwares which in my vie= w will do a good job. While searching I have unidentified the following as = viable softwares;
> abinit
> siesta
> quantum espresso =A0.
>
> I have started my calculations using abinit, but by the looks of it , = as the system is large it will take quite a time to optimize. I do like to = know your input on this matter. You might have much more experience in hand= ling these softwares and would like to know from above which can be conside= red a better choice?
>
> Thank you very much for your input and it's highly appreciated. >
> Neranjan>
>



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--
Neranjan Perera
Graduate Student
Department of Chemistry
University of Connectic= ut
55 North Eagleville Road
Unit 3060
storrs, CT 06269



--
Esteban Gabriel = Vega Hissi
=C1rea de Qu=EDmica F=EDsica
Departamento de Qu=EDmica
= Universidad Nacional de San Luis
Argentina

--90e6ba53a4a850963f04a87454a6--