From owner-chemistry@ccl.net Wed Jul 20 00:47:00 2011 From: "rocky walden rocky.walden19|,|gmail.com" To: CCL Subject: CCL: software to optimize a large molecule Message-Id: <-45111-110720004307-5166-R52M2q9IhSYpGZYYHL6uBA^^^server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=0016361e7a84c89e4b04a878ddd5 Date: Wed, 20 Jul 2011 10:12:57 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19[a]gmail.com] --0016361e7a84c89e4b04a878ddd5 Content-Type: text/plain; charset=ISO-8859-1 Hi Neranjan, The molecule you are working with 350 atoms is pretty small in comparison with (biomolecules) but the exception you have is a Metal atom. Optimization of the molecule whhich has a metal ion is a pretty much difficult ( as we need to have a defined forcefields for the Metal atoms ) In my opinion COMPASS (from Material Studios) have some set of defined force fields for the metal atoms. I hope now OPLS 2005 ( as this handles metal atoms in Glide docking) is also in a state to handle metal atoms. Yeah with Abinit , you seem to be working in core with DFT therory of optimization, which is computationally exhaustive and needs pretty good amount of time and disk space to run. I suggest you to try out 1st minimization with OPLS (2005) / COMPASS forcefields then opt for second round of optimization /minization with Abinit / Quantum Espresso. Happy minimization Thanks Walden On Wed, Jul 20, 2011 at 12:32 AM, Neranjan Perera neranjan007+/-gmail.com < owner-chemistry.:.ccl.net> 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> > > --0016361e7a84c89e4b04a878ddd5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Neranjan,
The molecule you are working with 350 atoms is pretty small in=20 comparison with (biomolecules) but the exception you have is a Metal=20 atom.
Optimization of the molecule whhich has a metal ion is a pretty much=20 difficult ( as we need to have a defined forcefields for the Metal atoms )
In my opinion COMPASS (from Material Studios) have some set of defined forc= e fields for the metal atoms.
I hope now OPLS 2005 ( as this handles metal atoms in Glide docking)=A0 is = also in a state to handle metal atoms.

Yeah with Abinit , you seem to be working in core with DFT therory of=20 optimization, which is computationally exhaustive and needs pretty good=20 amount of time and disk space to run.

I suggest you to try out 1st minimization with OPLS (2005) / COMPASS forcef= ields then opt for second round of optimization /minization with Abinit /=20 Quantum Espresso.

Happy minimization

Thanks
Walden

On Wed, Jul 20, 2011 at 12:32 AM, = Neranjan Perera neranjan007+/-gmail.com <owner-chemis= try.:.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 atoms, = including metal atoms. I have found following softwares which in my view wi= ll do a good job. While searching I have unidentified the following as viab= le softwares;
abinit
siesta
quantum espresso =A0.

I have started my calculations using abinit, but by the looks of it , as th= e 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



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--0016361e7a84c89e4b04a878ddd5-- From owner-chemistry@ccl.net Wed Jul 20 01:21:00 2011 From: "psavita(~)crlindia.com" To: CCL Subject: CCL: software to optimize a large molecule Message-Id: <-45112-110720005707-18576-2Z2evf40bvRHciCvbCNepA*_*server.ccl.net> X-Original-From: psavita..crlindia.com Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Wed, 20 Jul 2011 10:32:23 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita() crlindia.com
Hello N= eranjan,

It seems you need to optimize this large molecule having no= periodic boundaries. So it
is going to be compute intensive for any so= ftware, whether that employs plane waves
(as in abinit and QE) or Gaussi= ans (GAMESS). For large systems, it may be better to use
semiempirical (= such as MOPAC) or MM (such as GULP) prior to full ab initio optimization.On the other hand, if your system is describable with a unit cell with fe= w atoms, abinit or QE will be very fast.

Your question may be fully = answered if the system is properly understood.

Best wishes,

<= br>
= Savita Pundlik
Computational Materials Applied Research Group
Computational Res= earch Laboratories Ltd.,
Taco House, Daml= e Path, Off Law College Road
Pune - 411004, India.


=
= From owner-chemistry@ccl.net Wed Jul 20 05:44:00 2011 From: "Paul Fleurat-Lessard Paul.Fleurat-Lessard%ens-lyon.fr" To: CCL Subject: CCL:G: software to optimize a large molecule Message-Id: <-45113-110720030951-13153-FZTTgN0XTxTZiNiJgQRmpg=server.ccl.net> X-Original-From: Paul Fleurat-Lessard Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 20 Jul 2011 09:09:33 +0200 MIME-Version: 1.0 Sent to CCL by: Paul Fleurat-Lessard [Paul.Fleurat-Lessard__ens-lyon.fr] Hi, It seems that you want to use DFT. I think that one option not yet mentionned would be to use a QM:QM' or QM:MM approach. With this hybrid scheme you can use DFT for the metal and its close surrounding and then either a semi-empirical or MM level for the rest of the molecule. Concerning the geometry optimization efficiency, in my experience, Gaussian is really good for this task, but it is not free. In any case, it might be a good option to pre-optimize using a 'low-cost' level such as semi-empirical or MM, and the you can optimize the molecule at the DFT level if you need. Regards, paul. Le 20/07/2011 07:02, psavita(~)crlindia.com a crit : > Sent to CCL by: psavita() crlindia.com > Hello Neranjan, > > It seems you need to optimize this large molecule having no periodic boundaries. > So it > is going to be compute intensive for any software, whether that employs plane waves > (as in abinit and QE) or Gaussians (GAMESS). For large systems, it may be better > to use > semiempirical (such as MOPAC) or MM (such as GULP) prior to full ab initio > optimization. > On the other hand, if your system is describable with a unit cell with few > atoms, abinit or QE will be very fast. > > Your question may be fully answered if the system is properly understood. > > Best wishes, > > > Savita Pundlik > Computational Materials Applied Research Group > Computational Research Laboratories Ltd., > Taco House, Damle Path, Off Law College Road > Pune - 411004, India. > > > -=his is automatically added to each message by the mailing script =- To recover > the email address of the author of the message, please change the strange > characters on the top line to the -$- sign. You can also look up the > X-Original-From: line in the mail header. E-mail to subscribers: > CHEMISTRY-$-ccl.net or use:E-mail > to administrators: CHEMISTRY-REQUEST-$-ccl.net or useBefore posting, check wait time at: > http://www.ccl.netConferences: > http://server.ccl.net/chemistry/announcements/conferences/ Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml If your mail bounces from CCL > with 5.7.1 error, check:RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ -- Fleurat-Lessard Paul, Associate Professor Laboratoire de Chimie e-mail: Paul.Fleurat-Lessard-$-ens-lyon.fr Ecole Normale Suprieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Alle d'Italie Fax: + 33 (0)4 72 72 88 60 69364 Lyon Cedex 07 From owner-chemistry@ccl.net Wed Jul 20 08:58:00 2011 From: "Gkourmpis, Thomas Thomas.Gkourmpis.*|*.borealisgroup.com" To: CCL Subject: CCL:G: molecular geometry visualization on GaussView Message-Id: <-45114-110720015749-28867-x/DI9dy06er9F1Z7VOcGag*|*server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 20 Jul 2011 07:57:36 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis : borealisgroup.com] Hyunbok Hi Regarding your first question I would say that the differences you see are just rounding errors due to the way the software handles the geometry. Don't forget than no matter how you do the calculation Gaussian uses internal coordinates (by default at least unless you changed this), thus when these coordinates have to be translated into Cartesians some level of rounding errors for large numbers is expected. Personally I wouldn't be bother with differences of the order of 10-7 , as these are well within the uncertainty of the actual calculation. Regarding the second question Gaussian has two different ways of defining atomic bonds. One is via the distance between the two nuclei based on some internal tables that let the program know what to expect and how to interpret atoms at certain distance levels and second via the atomic connectivity defined by the user. If you setup the connectivity in GaussView when you prepare the job and save it to the input file (geom=connectivity) then GaussView will present these bonds as the type of bonds you set up despite the distance between the atoms. With respect to the actual distance the small differences have to do probably with the way the calculation is done. If these differences are really small I would not be alarmed about it. Obviously you know your system best, so I might be mistaken here. Regarding editing the bond from the chk file you can do this using the bond edit tools that GaussView has, although you will probably need to freeze the bond in the distance you require using modredundant coordinates and run a single point calculation to get the new energy. Ideally if the distance difference is only due to rounding errors from the coordinate system the energy differences should be really small. I hope this helps Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com^^^ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com^^^ccl.net] On Behalf Of Hyunbok Lee mutebeat*gmail.com Sent: Sunday, July 17, 2011 6:09 AM To: Gkourmpis, Thomas Subject: CCL:G: molecular geometry visualization on GaussView 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 Leehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis Email and any files transmitted with it are confidential and intended solely for the use of the individual or the entity to whom it is addressed. If you have received this Email by error, please notify the sender and delete the material from any storage device. Borealis extends no warranties and makes no representations as to the accuracy or completeness of the information provided. It is the customer's responsibility to inspect and test our products and technical advice in order to satisfy itself as to the suitability of the products and technical advice for the customer's particular purpose. From owner-chemistry@ccl.net Wed Jul 20 09:33:00 2011 From: "eurisco1^pochta.ru" To: CCL Subject: CCL: software to optimize a large molecule Message-Id: <-45115-110720044048-11761-//p99zzndu1ozB7RkX70eA/a\server.ccl.net> X-Original-From: Content-Type: multipart/alternative; boundary="----=_NextPart_000_004C_01CC46DA.3E4E3770" Date: Wed, 20 Jul 2011 12:40:44 +0400 MIME-Version: 1.0 Sent to CCL by: [eurisco1%pochta.ru] ]rn  qnnayemhe hg meqjnk|jhu w`qrei b tnpl`re MIME. ------=_NextPart_000_004C_01CC46DA.3E4E3770 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Neranjan Perera, Large enough molecules with large enough basis set may need software = with RI/DF-DFT. Maybe ORCA is suitable with its RIJCOSX approxiamtion = and free. Other programs can work for RI/DF-DFT, e.g. TURBOMOLE, etc. Sincerely, Ol Ga > From: neranjan perera neranjan007^gmail.com=20 Sent: Wednesday, July 20, 2011 1:45 AM To: Ga, Ol =20 Subject: CCL: software to optimize a large molecule 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 = 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> > -=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 usehttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: = http://server.ccl.net/chemistry/announcements/conferences/http://www.ccl.net/spammers.txt--=20 Neranjan Perera Graduate Student Department of Chemistry University of Connecticut 55 North Eagleville Road Unit 3060 storrs, CT 06269 ------=_NextPart_000_004C_01CC46DA.3E4E3770 Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Neranjan Perera,
 
Large enough molecules with large enough basis set may need = software with=20 RI/DF-DFT. Maybe ORCA is suitable with its RIJCOSX approxiamtion and = free. Other=20 programs can work for RI/DF-DFT, e.g. TURBOMOLE, etc.
 
Sincerely,
Ol Ga
 
 
 
Sent: Wednesday, July 20, 2011 1:45 AM
Subject: CCL: software to optimize a large=20 molecule
 
Yes,=20 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>= =20 wrote:

Sent to CCL by: Arne Dieckmann [adieckma[]googlemail.com]
It depends=20 on the level of theory you would like to apply. What would that be?=20 DFT?

Arne

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

>
>=20 Sent to CCL by: "Neranjan  Perera" [neranjan007#gmail.com]
> Hi = CCL=20 users,
>   I have a task of optimizing a molecule, = which has=20 close to 350 atoms, including metal atoms. I have found following = softwares=20 which in my view will do a good job. While searching I have = unidentified the=20 following as viable softwares;
> abinit
> siesta
> = quantum=20 espresso  .
>
> I have started my calculations using = abinit,=20 but by the looks of it , as the system is large it will take quite a = time to=20 optimize. I do like to know your input on this matter. You might have = much=20 more experience in handling these softwares and would like to know = > from above=20 which can be considered a better choice?
>
> Thank you = very much=20 for your input and it's highly appreciated.
>
>=20 Neranjan>
>



-=3D This is automatically added = to each=20 message by the mailing script =3D-



E-mail to = subscribers: CHEMISTRY++ccl.net or=20 use:
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--
Neranjan Perera
Graduate Student
Department of Chemistry
University of=20 Connecticut
55 North Eagleville Road
Unit 3060
storrs, CT=20 06269
 
------=_NextPart_000_004C_01CC46DA.3E4E3770-- From owner-chemistry@ccl.net Wed Jul 20 10:08:00 2011 From: "Olasunkanmi Lukman Olawale walecomuk*yahoo.co.uk" To: CCL Subject: CCL: opensource software Message-Id: <-45116-110720042313-17291-uQ89lm/TZIL0Re3zj6u2pg,,server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="0-366596398-1311150185=:58179" Date: Wed, 20 Jul 2011 09:23:05 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk:_:yahoo.co.uk] --0-366596398-1311150185=:58179 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello everyone,=0APlease I need you to=A0supply me with=A0the links to open= source softwares that can =0Acalculate thermodynamic properties for metals = and metal ions in gas phase and in =0Asolution. I will=A0prefer windows com= partible softwares.=0AThank you in anticipation.=0A=A0Olasunkanmi Lukman Ol= awale=0A________________________________=0ACurrent Address:=0ADepartment of= Chemistry,=0AObafemi Awolowo University,=0AIle-Ife, Osun State.=0ANigeria.= =0A=0A+234-0-80-52401564 Or +234-0-80-67161091=0A__________________________= ______=0A --0-366596398-1311150185=:58179 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A
Hello everyone,
=0A
Please I ne= ed you to supply me with the links to opensource softwares that c= an calculate thermodynamic properties for metals and metal ions in gas phas= e and in solution. I will prefer windows compartible softwares.
= =0A
Thank you in anticipation.
 
Olasunkanmi Lukman Olawale
=0A
=0ACurr= ent Address:
Department of Chemistry,
Obafemi = Awolowo University,
Ile-Ife, Osun St= ate.
Nigeria.
=0A
+234-0-80-52401564 Or +234-0-80-67161091
=0A
=0A
=0A
--0-366596398-1311150185=:58179-- From owner-chemistry@ccl.net Wed Jul 20 10:43:00 2011 From: "Horkel, Ernst ehorkel=ioc.tuwien.ac.at" To: CCL Subject: CCL:G: AW: G: Questions how to calculate Hyperpolarizability using G09 Message-Id: <-45117-110720095138-27913-xh3hOv/sIgYgiUQ1f7EwCQ^^^server.ccl.net> X-Original-From: "Horkel, Ernst" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 20 Jul 2011 15:51:26 +0200 MIME-Version: 1.0 Sent to CCL by: "Horkel, Ernst" [ehorkel%a%ioc.tuwien.ac.at] Dear Youzhao, Thank you for your hint, this guided me to do the job :-) However, it took me some time to figure out a working procedure. So I would like to share this with you all: A mini howto to get Hyperpolarizability with g09 For HF calcs you have to submit: “#p freq rhf/6-31g geom=connectivity polar”. For DFT calcs you have to submit “#p opt freq=raman b3lyp/6-31g geom=connectivity polar” Nota bene that you have to add the "raman" option when using DFT! For more information (e.g. when using MP2 etc) one has to check the Gaussian manual, keywords “FREQ” and “POLAR” The information in the output is located at the section reading similar to: Dipole = 2.37312183D-16 -6.66133815D-16 -9.39281319D-01 Polarizability= 7.83427191D-01 1.60008472D-15 6.80285860D+00 -3.11369582D-17 2.72397709D-16 3.62729494D+00 HyperPolar = 3.08796953D-16 -6.27350412D-14 4.17080415D-16 5.55019858D-14 -7.26773439D-01 -1.09052038D-14 -2.07727337D+01 4.49920497D-16 -1.40402516D-13 -1.10991697D+01 As Youzhao already wrote... Univ.Ass. Dipl.-Ing. Dr.techn. Ernst Horkel Institute of Applied Synthetic Chemistry, Vienna University of Technology          Tel.: +43-1-58801-163609 Getreidemarkt 9/163OC,                         +43-644-60588-7122 A-1060 Vienna, Austria                   Fax:  +43-1-58801-15499 email: ehorkel(!)ioc.tuwien.ac.at -----Ursprüngliche Nachricht----- Von: owner-chemistry+ehorkel==ioc.tuwien.ac.at(!)ccl.net [mailto:owner-chemistry+ehorkel==ioc.tuwien.ac.at(!)ccl.net] Im Auftrag von "Youzhao Lan (???)" lyzhao]_[zjnu.cn Gesendet: Dienstag, 12. Juli 2011 02:37 An: Horkel, Ernst Betreff: CCL:G: Questions how to calculate Hyperpolarizability using G09 Sent to CCL by: =?UTF-8?B?IllvdXpoYW8gTGFuICjok53lsKTpkoopIg==?= [lyzhao|-|zjnu.cn] Hi Ernst, The information you just located are not what you want. They would look like the following: " Dipole = 2.37312183D-16 -6.66133815D-16 -9.39281319D-01 Polarizability= 7.83427191D-01 1.60008472D-15 6.80285860D+00 -3.11369582D-17 2.72397709D-16 3.62729494D+00 HyperPolar = 3.08796953D-16 -6.27350412D-14 4.17080415D-16 5.55019858D-14 -7.26773439D-01 -1.09052038D-14 -2.07727337D+01 4.49920497D-16 -1.40402516D-13 -1.10991697D+01 "here 10 B_components" " more detail, please refer to "frequency" keyword in Gaussian help. Best regards. ======================================================== -------------------------------------------------------- Youzhao Lan Institute of Physical Chemistry, Department of Chemistry,College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, China. -------------------------------------------------------- 2011-07-09 ========================================================http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Jul 20 11:18:00 2011 From: "Turbomole Support Team turbomole[*]cosmologic.de" To: CCL Subject: CCL: TURBOMOLE 6.3 released Message-Id: <-45118-110720100258-5627-QYz9EfEQswUHZnTkqbt9iw~~server.ccl.net> X-Original-From: Turbomole Support Team Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 20 Jul 2011 16:02:44 +0200 MIME-Version: 1.0 Sent to CCL by: Turbomole Support Team [turbomole(!)cosmologic.de] Dear CCL Colleagues, TURBOMOLE: New Release 6.3 Enhancements include: - parallel version for multi-core/SMP systems for: -- 2nd analytic derivatives (frequencies) for HF, DFT and RI-DFT -- CCSD and CCSD(T) energies including symmetry -- UV/Vis, CD spectra and TDDFT/CC2/ADC(2) analytic gradients - restartable analytic frequency calculations - COSMO solvation model for TDDFT spectra - DFT + Dispersion in its latest version from the Grimme group - explicitly correlated CCSD(F12*) For further details see: *TURBOMOLE*: http://www.cosmologic.de/index.php?cosId=3050&crId=3 *TmoleX (GUI)*: The new release also includes the latest version of the graphical user interface TmoleX 3.2 as a free add-on to Turbomole with improved support for remote jobs (use TmoleX on your Windows, Mac or Linux desktop and run the jobs on remote Linux/Unix/MacOS machines and/or submit them to a queuing system on a remote Linux/Unix cluster). http://www.cosmologic.de/index.php?cosId=3015&crId=3 For licensing options and pricing contact your local supplier at http://www.cosmologic.de/index.php?cosId=1200&crId=1 Demo and time limited evaluation versions are available. Best regards, Uwe Huniar on behalf of the Turbomole Support Team From owner-chemistry@ccl.net Wed Jul 20 11:53:00 2011 From: "prema mahadev awati prema.a#iiserpune.ac.in" To: CCL Subject: CCL: viscosity Message-Id: <-45119-110720110352-32384-SyRiFbMDgTgNYq5qCWjzkw.@.server.ccl.net> X-Original-From: "prema mahadev awati" Date: Wed, 20 Jul 2011 11:03:49 -0400 Sent to CCL by: "prema mahadev awati" [prema.a##iiserpune.ac.in] I am working on ionic liquids MD simulation,actually I want to determine viscosity what I know can be obtained using g_energy in GROMACS but how to interprete those plots,i mean it gives three graphs;shear viscosity,bulk viscosity and one correlation graph,i am not able to understand this from manual,Please if anyone has done this or know about guide me,I will truly appreciate there for the help. Thanks. From owner-chemistry@ccl.net Wed Jul 20 12:28:00 2011 From: "prema mahadev awati prema.a###iiserpune.ac.in" To: CCL Subject: CCL: viscosity Message-Id: <-45120-110720111157-9193-6ty23C/ez9ysQ4yY9zRPgw*server.ccl.net> X-Original-From: "prema mahadev awati" Date: Wed, 20 Jul 2011 11:11:53 -0400 Sent to CCL by: "prema mahadev awati" [prema.a[A]iiserpune.ac.in] I am working on ionic liquids MD simulation,actually I want to determine viscosity what I know can be obtained using g_energy in GROMACS but how to interprete those plots,i mean it gives three graphs;shear viscosity,bulk viscosity and one correlation graph,i am not able to understand this from manual,Please if anyone has done this or know about guide me,I will truly appreciate there for the help. Thanks. From owner-chemistry@ccl.net Wed Jul 20 13:02:00 2011 From: "Tymofii N tim_mail=-=ukr.net" To: CCL Subject: CCL: Freeware with analytical Hessian after DFT geometry optimization Message-Id: <-45121-110720115335-20206-7KoGQUUVCjowDJh1OzMCtA|-|server.ccl.net> X-Original-From: "Tymofii N" Date: Wed, 20 Jul 2011 11:53:28 -0400 Sent to CCL by: "Tymofii N" [tim_mail!A!ukr.net] Could anyone advice me some _free_ software package capable for DFT geometry optimization (with B3LYP or its dispersion-corrected versions) _AND_ subsequent _analytical_ Hessian calculation (i.e., with no numerical differentiation of gradients)for vibrational analysis ? Thank you in advance! Tymofii From owner-chemistry@ccl.net Wed Jul 20 14:14:00 2011 From: "Alfredo Mayall Simas simas|*|ufpe.br" To: CCL Subject: CCL: Research Trends and the Future of Computational Chemistry Message-Id: <-45122-110720141030-23129-vHw37uiVNlpHiuGnaViDIA%%server.ccl.net> X-Original-From: "Alfredo Mayall Simas" Date: Wed, 20 Jul 2011 14:10:27 -0400 Sent to CCL by: "Alfredo Mayall Simas" [simas^-^ufpe.br] Dear CCL, I am preparing a plenary lecture for our Brazilian Theoretical Chemistry Symposium, which will take place here by late November. I would appreciate if any of you could share, with all of us, your thoughts on the future of theoretical and computational chemistry. Major themes of interest would be, for example: (i) The major problems being tackled right now; (ii) The unfolding research trends; (iii) The expected developments that will most likely take place in the near future; and, (iv) The expected developments that should take place and which would represent a significant advance in theoretical and computational chemistry research. Besides, if you know any articles on these topics - both scientific and press articles - I would appreciate receiving information on them. Thank you all in advance for your help and for sharing your visions! Sincerely, Alfredo Mayall Simas Recife, PE, Brazil http://www.sparkle.pro.br http://www.rm1.sparkle.pro.br From owner-chemistry@ccl.net Wed Jul 20 14:49:01 2011 From: "dipankar roy theodip[*]gmail.com" To: CCL Subject: CCL: Freeware with analytical Hessian after DFT geometry optimization Message-Id: <-45123-110720143110-7719-WJyp07eESrReU0/9qS5pmg^-^server.ccl.net> X-Original-From: dipankar roy Content-Type: multipart/alternative; boundary=bcaec51a72a83c8e9b04a8846f9a Date: Wed, 20 Jul 2011 14:31:02 -0400 MIME-Version: 1.0 Sent to CCL by: dipankar roy [theodip+/-gmail.com] --bcaec51a72a83c8e9b04a8846f9a Content-Type: text/plain; charset=ISO-8859-1 Hi, You may try ORCA. best, Dipankar Roy On Wed, Jul 20, 2011 at 11:53 AM, Tymofii N tim_mail=-=ukr.net < owner-chemistry(0)ccl.net> wrote: > > Sent to CCL by: "Tymofii N" [tim_mail!A!ukr.net] > Could anyone advice me some _free_ software package capable for > DFT geometry optimization (with B3LYP or its dispersion-corrected versions) > _AND_ subsequent _analytical_ Hessian calculation (i.e., with no numerical > differentiation of gradients)for vibrational analysis ? > Thank you in advance! > Tymofii> > > -- ----------------------------------- Dr. Dipankar Roy Research Associate Hunter College (CUNY) 695 Park Avenue New York, USA NY-10065 ----------------------------------- --bcaec51a72a83c8e9b04a8846f9a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

You may try ORCA.

best,
Dipankar Roy=A0

On Wed, Jul 20, 20= 11 at 11:53 AM, Tymofii N tim_mail=3D-=3Dukr.net= <owner= -chemistry(0)ccl.net> wrote:

Sent to CCL by: "Tymofii =A0N" [tim_mail!A!ukr.net]
Could anyone advice me some _free_ software package capable for
DFT geometry optimization (with B3LYP or its dispersion-corrected versions)=
_AND_ subsequent _analytical_ Hessian calculation (i.e., with no numerical = differentiation of gradients)for vibrational analysis ?
Thank you in advance!
Tymofii



-=3D This is automatically added to each message by the mailing script =3D-=
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--
-----------------------= ------------
Dr. Dipankar Roy
Research Associate
Hu= nter College (CUNY)
695 Park Avenue
New York, USA
NY-10065
-----------------------------------

--bcaec51a72a83c8e9b04a8846f9a-- From owner-chemistry@ccl.net Wed Jul 20 16:23:01 2011 From: "Tymofii Nikolaienko tim_mail:-:ukr.net" To: CCL Subject: CCL: Freeware with analytical Hessian after DFT geometry optimization Message-Id: <-45124-110720162033-5196-ofJpuvyGrxbJnMT9VgMt2A---server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Type: multipart/alternative; boundary="------------060306020203080207010905" Date: Wed, 20 Jul 2011 23:20:16 +0300 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail|ukr.net] This is a multi-part message in MIME format. --------------060306020203080207010905 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear Roy ! I'm not sure that ORCA can really make analytical Hessian for DFT... Here is a text from the latest ORCA 2.8.0 documentation: "6.3 Vibrational Frequencies Vibrational frequency calculations are available through one- or two- sided _numerical differentiation_ of analytical gradients, i.e. for Hartree-Fock and DFT models." Best regards, Tymofii 20.07.2011 21:31, dipankar roy theodip[*]gmail.com wrote: > Hi, > > You may try ORCA. > > best, > Dipankar Roy > > On Wed, Jul 20, 2011 at 11:53 AM, Tymofii N tim_mail=-=ukr.net > > wrote: > > > Sent to CCL by: "Tymofii N" [tim_mail!A!ukr.net ] > Could anyone advice me some _free_ software package capable for > DFT geometry optimization (with B3LYP or its dispersion-corrected > versions) > _AND_ subsequent _analytical_ Hessian calculation (i.e., with no > numerical differentiation of gradients)for vibrational analysis ? > Thank you in advance! > Tymofii > > > > -= This is automatically added to each message by the mailing > script =- > > > > E-mail to subscribers: CHEMISTRY- -ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST- -ccl.net > or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > -- > ----------------------------------- > Dr. Dipankar Roy > Research Associate > Hunter College (CUNY) > 695 Park Avenue > New York, USA > NY-10065 > ----------------------------------- > --------------060306020203080207010905 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Roy !

I'm not sure that ORCA can really make analytical Hessian for DFT...
Here is a text from the latest ORCA 2.8.0 documentation:
"6.3 Vibrational Frequencies
Vibrational frequency calculations are available through one-­ or two-­ sided
_numerical differentiation_ of analytical gradients, i.e. for Hartree-­Fock and DFT models."


Best regards,
Tymofii



20.07.2011 21:31, dipankar roy theodip[*]gmail.com wrote:
Hi,

You may try ORCA.

best,
Dipankar Roy 

On Wed, Jul 20, 2011 at 11:53 AM, Tymofii N tim_mail=-=ukr.net <owner-chemistry- -ccl.net> wrote:

Sent to CCL by: "Tymofii  N" [tim_mail!A!ukr.net]
Could anyone advice me some _free_ software package capable for
DFT geometry optimization (with B3LYP or its dispersion-corrected versions)
_AND_ subsequent _analytical_ Hessian calculation (i.e., with no numerical differentiation of gradients)for vibrational analysis ?
Thank you in advance!
Tymofii





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--
-----------------------------------
Dr. Dipankar Roy
Research Associate
Hunter College (CUNY)
695 Park Avenue
New York, USA
NY-10065
-----------------------------------

--------------060306020203080207010905-- From owner-chemistry@ccl.net Wed Jul 20 18:48:00 2011 From: "Kalju Kahn kalju-$-chem.ucsb.edu" To: CCL Subject: CCL: Freeware with analytical Hessian after DFT geometry optimization Message-Id: <-45125-110720184512-5436-M1KRsGzBEzK7GaR5QiBFzw .. server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 20 Jul 2011 15:44:53 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju-#-chem.ucsb.edu] Tymofii, 1) NWChem 6.0 for closed shell only; does not use symmetry. Have not tried myself but that's what the manual says. 2) Maybe the development/beta version of Firefly. Analytical DFT second derivatives have been on the "current activity" category for quite some time. If it works, it is likely to be quite fast but you are limited to basis sets with s,p,d,f,g shells. You can inquire in their list for details. Hope that helps, Kalju > > Sent to CCL by: "Tymofii N" [tim_mail!A!ukr.net] > Could anyone advice me some _free_ software package capable for > DFT geometry optimization (with B3LYP or its dispersion-corrected > versions) > _AND_ subsequent _analytical_ Hessian calculation (i.e., with no numerical > differentiation of gradients)for vibrational analysis ? > Thank you in advance! > Tymofii> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106