From owner-chemistry@ccl.net Wed Mar 20 00:31:01 2013 From: "Geoffrey Hutchison geoffh~~pitt.edu" To: CCL Subject: CCL:G: Optimizing Fragments with 6 Degrees of Freedom Message-Id: <-48437-130320002737-16577-pQ5qXSVebfTu2P7KCHQRcw],[server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Wed, 20 Mar 2013 00:27:38 -0400 MIME-version: 1.0 (Mac OS X Mail 6.3 \(1503\)) Sent to CCL by: Geoffrey Hutchison [geoffh]^[pitt.edu] I have a bit of a strange request. I'm looking to do a geometry optimization between two "frozen" molecular fragments. I'm using Gaussian, but any other modern DFT program would be fine. Consider, for example, optimizing benzene dimer. There are multiple local minima. And yes, the benzene geometry relaxes. But I mainly want to optimize the intermolecular distances and angles (i.e., 6 degrees of freedom). In principal, you should be able to do this with Gaussian's ModRedundant, but the obvious constraints haven't worked. I tried freezing with wildcards and *everything* was frozen. Since there are two benzenes, I don't really want to list 36 constraints if I can avoid it. (Yes, if all else fails, I'll write a script to generate the appropriate constraints. But this seems like a useful thing to ask for posterity.) Any creative ideas (or alternate programs)? Thanks very much, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh-$-pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Wed Mar 20 03:33:00 2013 From: "Ulrike Salzner salzner[A]gmail.com" To: CCL Subject: CCL:G: Optimizing Fragments with 6 Degrees of Freedom Message-Id: <-48438-130320032758-24491-+U5AKrJKf0UwziNjq9tGUA|server.ccl.net> X-Original-From: Ulrike Salzner Content-Type: multipart/alternative; boundary=bcaec5523fe8fde6d004d85628c0 Date: Wed, 20 Mar 2013 09:27:53 +0200 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner===gmail.com] --bcaec5523fe8fde6d004d85628c0 Content-Type: text/plain; charset=ISO-8859-1 Dear Geoff, have you tried POPT and using Z-matrix? The first set of parameters are variables and after a blank line you put the constants.That should work. Regards, Ulrike On Wed, Mar 20, 2013 at 6:27 AM, Geoffrey Hutchison geoffh~~pitt.edu < owner-chemistry=ccl.net> wrote: > > Sent to CCL by: Geoffrey Hutchison [geoffh]^[pitt.edu] > I have a bit of a strange request. I'm looking to do a geometry > optimization between two "frozen" molecular fragments. I'm using Gaussian, > but any other modern DFT program would be fine. > > Consider, for example, optimizing benzene dimer. There are multiple local > minima. And yes, the benzene geometry relaxes. But I mainly want to > optimize the intermolecular distances and angles (i.e., 6 degrees of > freedom). > > In principal, you should be able to do this with Gaussian's ModRedundant, > but the obvious constraints haven't worked. I tried freezing with wildcards > and *everything* was frozen. Since there are two benzenes, I don't really > want to list 36 constraints if I can avoid it. (Yes, if all else fails, > I'll write a script to generate the appropriate constraints. But this seems > like a useful thing to ask for posterity.) > > Any creative ideas (or alternate programs)? > > Thanks very much, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geoffh()pitt.edu > web: http://hutchison.chem.pitt.edu/> > > -- Assoc. Prof. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara --bcaec5523fe8fde6d004d85628c0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Geoff,
have you tried POPT an= d using Z-matrix? The first set of parameters are variables and after a bla= nk line you put the constants.That should work.
Regards,
Ulrike


On Wed, Mar 20, 2013 at 6:27 AM, Geoffrey Hutchison geoffh~~pitt.edu <owner-chemistry=ccl.net>= wrote:

Sent to CCL by: Geoffrey Hutchison [geoffh]^[pitt.edu]
I have a bit of a strange request. I'm looking to do a geometry optimiz= ation between two "frozen" molecular fragments. I'm using Gau= ssian, but any other modern DFT program would be fine.

Consider, for example, optimizing benzene dimer. There are multiple local m= inima. And yes, the benzene geometry relaxes. But I mainly want to optimize= the intermolecular distances and angles (i.e., 6 degrees of freedom).

In principal, you should be able to do this with Gaussian's ModRedundan= t, but the obvious constraints haven't worked. I tried freezing with wi= ldcards and *everything* was frozen. Since there are two benzenes, I don= 9;t really want to list 36 constraints if I can avoid it. (Yes, if all else= fails, I'll write a script to generate the appropriate constraints. Bu= t this seems like a useful thing to ask for posterity.)

Any creative ideas (or alternate programs)?

Thanks very much,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648= -0492
email: geoffh()pitt.edu web: http://h= utchison.chem.pitt.edu/



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--
Assoc. Prof. Ulrike Sal= zner
Department of Chemistry
Bilkent University
06800 Bilkent, Ank= ara
--bcaec5523fe8fde6d004d85628c0-- From owner-chemistry@ccl.net Wed Mar 20 10:38:01 2013 From: "Fedor Goumans goumans-x-scm.com" To: CCL Subject: CCL:G: Optimizing Fragments with 6 Degrees of Freedom Message-Id: <-48439-130320085355-19014-zxPkld6sLH5WPTvgKCowpA~!~server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 20 Mar 2013 13:52:46 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans _ scm.com] Dear Geoff, Treating two rigid blocks as geometry entities that can move with respect to each other, but are otherwise frozen, is exactly what the Mobile Block Hessian (MBH) method was designed to do (although in this case especially for frequency analysis). This method was developed by An Ghysels during her PhD with Prof. van Waroquier at Ghent University: http://molmod.ugent.be/thesis/development-accurate-and-efficient-method-normal-mode-analysis-extended-molecular-systems In ADF, where An has also implemented her MBH method, one can also optimize two rigid blocks using block constraints. It's really easy to set up such a calculation in the ADFGUI by assigning each benzene ring to its own region and setting block constraints for each. (I post step-by-step instructions below in case you want to try out for yourself with a 30-day free evaluation of our software). If you prefer command-line editing you, it is equally straightforward to assign these two regions and defining a block constraint for each of them. For your benzene dimer examples you may also find it useful that ADF has the latest dispersion-corrected functionals available (e.g. Grimme's D3 with Becke-Johnson damping and Steinman & Corminboeuf's dDsC). Hope this helps, Fedor Step-by-step set up of a frozen benzene - frozen benzene geometry optimization with block constraints in ADF 1. Create a benzene dimer in ADFinput, and define two regions If you import coordinates you will have regions defined automatically for each imported molecule. It's easiest if you use the search function (magnifying glass top left) and select Benzene (ADF) from the molecule results. Do this again to import a second benzene, you can move this one (it is selected) with respect to the other by clicking on the molecule while holding shift (left button for rotate, right for translate) and moving it with the mouse where you want to have it. Rename the region names to Benzene1 and Benzene2 for clarity. Alternatively, just build two benzene molecules yourself with the other build tools. Then you will have to define a region for each one in the Model -> Regions panel: select the first benzene, click '+' and do the same for the second. 2. Choose the "Geometry Optimization" preset on the Main input panel You want to define your (dispersion-corrected) functional and basis set here as well. 3. Go to the Model -> 'Geometry constraints and scan' input panel 4. Define block constraints: Select any atom from the first benzene, and click the '+' next to "Benzene1 (block)" Select any atom from the second benzene, and click the '+' next to "Benzene2 (block)" 5. Run This is a constrained optimization job with two frozen blocks, just as requested. Should any atoms be outside a frozen block, their positions will be fully optimized. On 3/20/2013 5:27 AM, Geoffrey Hutchison geoffh~~pitt.edu wrote: > Sent to CCL by: Geoffrey Hutchison [geoffh]^[pitt.edu] > I have a bit of a strange request. I'm looking to do a geometry optimization between two "frozen" molecular fragments. I'm using Gaussian, but any other modern DFT program would be fine. > > Consider, for example, optimizing benzene dimer. There are multiple local minima. And yes, the benzene geometry relaxes. But I mainly want to optimize the intermolecular distances and angles (i.e., 6 degrees of freedom). > > In principal, you should be able to do this with Gaussian's ModRedundant, but the obvious constraints haven't worked. I tried freezing with wildcards and *everything* was frozen. Since there are two benzenes, I don't really want to list 36 constraints if I can avoid it. (Yes, if all else fails, I'll write a script to generate the appropriate constraints. But this seems like a useful thing to ask for posterity.) > > Any creative ideas (or alternate programs)? > > Thanks very much, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geoffh()pitt.edu > web: http://hutchison.chem.pitt.edu/> > -- Dr. T. P. M. Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans*scm.com http://www.scm.com From owner-chemistry@ccl.net Wed Mar 20 11:12:01 2013 From: "Daniel Fernando Coimbra danielfcoimbra**gmail.com" To: CCL Subject: CCL:G: Optimizing Fragments with 6 Degrees of Freedom Message-Id: <-48440-130320104244-27211-D7zuo+GS+2jQeIZKLozYSQ{=}server.ccl.net> X-Original-From: Daniel Fernando Coimbra Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 20 Mar 2013 11:42:33 -0300 MIME-Version: 1.0 Sent to CCL by: Daniel Fernando Coimbra [danielfcoimbra],[gmail.com] ORCA can easily do this. You can define two fragments and specify that thei are constrained but that their "connection" is to be optimized. You define each atoms fragment number by putting "(1)" or "(2)" at the coords, after the atom, and use the likes of "ConnectFragments {1 2 C 12 28}" and "invertConstraints true" (this will optimize the connection between fragments 1 and 2, connected by atoms 12 and 28, freezing everything else) as detailed in the manual. Em 20/03/2013 01:27, Geoffrey Hutchison geoffh~~pitt.edu escreveu: > > Sent to CCL by: Geoffrey Hutchison [geoffh]^[pitt.edu] > I have a bit of a strange request. I'm looking to do a geometry optimization between two "frozen" molecular fragments. I'm using Gaussian, but any other modern DFT program would be fine. > > Consider, for example, optimizing benzene dimer. There are multiple local minima. And yes, the benzene geometry relaxes. But I mainly want to optimize the intermolecular distances and angles (i.e., 6 degrees of freedom). > > In principal, you should be able to do this with Gaussian's ModRedundant, but the obvious constraints haven't worked. I tried freezing with wildcards and *everything* was frozen. Since there are two benzenes, I don't really want to list 36 constraints if I can avoid it. (Yes, if all else fails, I'll write a script to generate the appropriate constraints. But this seems like a useful thing to ask for posterity.) > > Any creative ideas (or alternate programs)? > > Thanks very much, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geoffh()pitt.edu > web: http://hutchison.chem.pitt.edu/ -- Daniel Fernando Coimbra Grupo de Estrutura Eletrônica Molecular Departamento de Química Universidade Federal de Santa Catarina From owner-chemistry@ccl.net Wed Mar 20 14:31:00 2013 From: "Mehe H Khan mehedi.acct ~ gmail.com" To: CCL Subject: CCL:G: Running crystal Structure Message-Id: <-48441-130320134708-8760-Rkx2r1upRdWUOSK9oyMdNw-,-server.ccl.net> X-Original-From: "Mehe H Khan" Date: Wed, 20 Mar 2013 13:47:07 -0400 Sent to CCL by: "Mehe H Khan" [mehedi.acct * gmail.com] Hello, I want to work with a reaction. one of the reactants is in crystal structure. But as far as i know gaussian works with gas phase. Is there any way that I can work with crystal structure in gaussian? Mehedi Hasan PhD student Jackson State University From owner-chemistry@ccl.net Wed Mar 20 15:06:00 2013 From: "mehedi mehedi.acct%a%gmail.com" To: CCL Subject: CCL:G: Crystal Structure Message-Id: <-48442-130320135219-9071-idjr5HF6EhHiYKDiQm8/BQ*server.ccl.net> X-Original-From: mehedi Content-Type: multipart/alternative; boundary=bcaec543072aa8d66d04d85ee12b Date: Wed, 20 Mar 2013 12:52:11 -0500 MIME-Version: 1.0 Sent to CCL by: mehedi [mehedi.acct,+,gmail.com] --bcaec543072aa8d66d04d85ee12b Content-Type: text/plain; charset=ISO-8859-1 Hello, I'm trying to work for the reaction with a crystal structure with another ligand. I intend to use gaussian. but i think gaussian work with gas phase only. is there any way that i can find if a reaction would happen at a certain temparature and pressure at the crystal structure in gaussian? Thanking -- Md. Mehedi Hasan Khan PhD Research Assistant Computational Chemistry Laboratory Jackson State University Jackson, MS, USA --bcaec543072aa8d66d04d85ee12b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,
I'm trying to work for the reaction with a crystal structure= with another ligand. I intend to use gaussian. but i think gaussian work w= ith gas phase only. is there any way that i can find if a reaction would ha= ppen at a certain temparature and pressure at the crystal structure in gaus= sian?

Thanking

--
Md= . Mehedi Hasan Khan
PhD Research Assistant
Computationa= l Chemistry Laboratory
Jackson State University
Jackson= , MS, USA
--bcaec543072aa8d66d04d85ee12b-- From owner-chemistry@ccl.net Wed Mar 20 15:40:00 2013 From: "Close, David M. CLOSED-*-mail.etsu.edu" To: CCL Subject: CCL:G: Running crystal Structure Message-Id: <-48443-130320151957-15406-Rvk/GIof0+lKu4W83LdwyA|server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 20 Mar 2013 19:19:42 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED:mail.etsu.edu] Mehedi: You have to explain what you want to do with the crystal structure. What properties are you interested in? If you mean the periodic properties, you have to use periodic code to simulate the crystal lattice. If you want the structure of a unit cell, you have to use the symmetry properties of the crystal to generate the positions of the molecules in the unit cell. I'm sure you can find answers here if you just give details on what you are interested in. Regards, Dave Close -----Original Message----- > From: owner-chemistry+closed==etsu.edu|-|ccl.net [mailto:owner-chemistry+closed==etsu.edu|-|ccl.net] On Behalf Of Mehe H Khan mehedi.acct ~ gmail.com Sent: Wednesday, March 20, 2013 1:47 PM To: Close, David M. Subject: CCL:G: Running crystal Structure Sent to CCL by: "Mehe H Khan" [mehedi.acct * gmail.com] Hello, I want to work with a reaction. one of the reactants is in crystal structure. But as far as i know gaussian works with gas phase. Is there any way that I can work with crystal structure in gaussian? Mehedi Hasan PhD student Jackson State Universityhttp://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 Mar 20 17:34:00 2013 From: "Susi Lehtola susi.lehtola~~alumni.helsinki.fi" To: CCL Subject: CCL:G: Running crystal Structure Message-Id: <-48444-130320163735-13482-rJnw5xQZ62aCGTzZRo5Q4g()server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Wed, 20 Mar 2013 22:37:22 +0200 Mime-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola**alumni.helsinki.fi] On Wed, 20 Mar 2013 13:47:07 -0400 "Mehe H Khan mehedi.acct ~ gmail.com" wrote: > > Sent to CCL by: "Mehe H Khan" [mehedi.acct * gmail.com] > Hello, > I want to work with a reaction. one of the reactants is in crystal > structure. But as far as i know gaussian works with gas phase. Is > there any way that I can work with crystal structure in gaussian? It can do periodic calculations (infinite system) as well http://www.gaussian.com/g_tech/g_ur/k_pbc.htm -- --------------------------------------------------------------- Mr. Susi Lehtola, PhD Postdoctoral researcher susi.lehtola{=}alumni.helsinki.fi Department of Applied Physics http://www.helsinki.fi/~jzlehtol Aalto university Finland --------------------------------------------------------------- Susi Lehtola, FT Tutkijatohtori susi.lehtola{=}alumni.helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Aalto-yliopisto --------------------------------------------------------------- From owner-chemistry@ccl.net Wed Mar 20 18:23:00 2013 From: "mehedi mehedi.acct..gmail.com" To: CCL Subject: CCL:G: Running crystal Structure Message-Id: <-48445-130320182219-13321-Zb3s4Ea0gbZ+IqK9/J4Jlg^^server.ccl.net> X-Original-From: mehedi Content-Type: multipart/alternative; boundary=bcaec543072a25231e04d862a793 Date: Wed, 20 Mar 2013 17:22:09 -0500 MIME-Version: 1.0 Sent to CCL by: mehedi [mehedi.acct~~gmail.com] --bcaec543072a25231e04d862a793 Content-Type: text/plain; charset=ISO-8859-1 thanks David for you reply. actually I wanted to know if two reactants will react at a certain temperature and pressure. suppose, I want to know if a crystal structure of NaCl will react with CaO at 330K temp. ant 2 atm. pressure. how do i do that? how do i do that? any kind of suggestion would be much appreciated. On Wed, Mar 20, 2013 at 2:19 PM, Close, David M. CLOSED-*-mail.etsu.edu < owner-chemistry+/-ccl.net> wrote: > > Sent to CCL by: "Close, David M." [CLOSED:mail.etsu.edu] > Mehedi: > You have to explain what you want to do with the crystal structure. > What properties are you interested in? If you mean the periodic > properties, you have to use periodic code to simulate the crystal lattice. > If you want the structure of a unit cell, you have to use the symmetry > properties of the crystal to generate the positions of the molecules in the > unit cell. > I'm sure you can find answers here if you just give details on what you > are interested in. > Regards, Dave Close > > -----Original Message----- > > From: owner-chemistry+closed==etsu.edu .. ccl.net [mailto: > owner-chemistry+closed==etsu.edu .. ccl.net] On Behalf Of Mehe H Khan > mehedi.acct ~ gmail.com > Sent: Wednesday, March 20, 2013 1:47 PM > To: Close, David M. > Subject: CCL:G: Running crystal Structure > > > Sent to CCL by: "Mehe H Khan" [mehedi.acct * gmail.com] Hello, I want to > work with a reaction. one of the reactants is in crystal structure. > But as far as i know gaussian works with gas phase. Is there any way that > I can work with crystal structure in gaussian? > > Mehedi Hasan > PhD student > Jackson State Universityhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > -- Md. Mehedi Hasan Khan PhD Research Assistant Computational Chemistry Laboratory Jackson State University Jackson, MS, USA --bcaec543072a25231e04d862a793 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable thanks David for you reply. actually I wanted to know if =A0two reactants w= ill react at a certain=A0temperature=A0and pressure. suppose, I want to kno= w if a crystal structure of NaCl will react with CaO at 330K temp. ant 2 at= m. pressure. how do i do that? how do i do that? any kind of suggestion wou= ld be much=A0appreciated.

On Wed, Mar 20, 2013 at 2:19 PM, Close, Davi= d M. CLOSED-*-mail.etsu.edu <o= wner-chemistry+/-ccl.net> wrote:

Sent to CCL by: "Close, David M." [CLOSED:mail.etsu.edu]
Mehedi:
=A0 You have to explain what you want to do with the crystal structure. =A0= What properties are you interested in? =A0If you mean the periodic properti= es, you have to use periodic code to simulate the crystal lattice. =A0If yo= u want the structure of a unit cell, you have to use the symmetry propertie= s of the crystal to generate the positions of the molecules in the unit cel= l.
I'm sure you can find answers here if you just give details on what you= are interested in.
=A0 Regards, Dave Close

-----Original Message-----
> From: owner-chemistry+closed=3D=3Detsu.edu .. cc= l.net [mailto:owner-chemist= ry+closed=3D=3Detsu.edu .. ccl.net] On Behalf O= f Mehe H Khan mehedi.acct ~ = gmail.com
Sent: Wednesday, March 20, 2013 1:47 PM
To: Close, David M.
Subject: CCL:G: Running crystal Structure


Sent to CCL by: "Mehe H Khan" [mehedi.acct * gmail.com] Hello, I want to work with a reac= tion. one of the reactants is in crystal structure.
But as far as i know gaussian works with gas phase. Is there any way that I= can work with crystal structure in gaussian?

Mehedi Hasan
PhD student
Jackson State Universityhttp://www.ccl.net/cgi-bin/ccl/send_ccl_me= ssagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammer= s.txt


-=3D This is automatically added to each message by the mailing script =3D-=
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--
=
Md. Mehedi Hasan Khan
PhD Research Assistant
Compu= tational Chemistry Laboratory
Jackson State University
Jackson, MS, USA
--bcaec543072a25231e04d862a793-- From owner-chemistry@ccl.net Wed Mar 20 22:00:01 2013 From: "Vasile Chis vasilechis**gmail.com" To: CCL Subject: CCL:G: Optimizing Fragments with 6 Degrees of Freedom Message-Id: <-48446-130320175545-1030-SckawE5ywiv+rksf5VhBng.:.server.ccl.net> X-Original-From: Vasile Chis Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 20 Mar 2013 23:55:07 +0200 MIME-Version: 1.0 Sent to CCL by: Vasile Chis [vasilechis##gmail.com] Dear Geoff, You can use dummy atoms to define the necessary coordinates for a partial optimization. The included example (see bellow) corresponds to a MnPc dimer for which a partial optimization (dx, dy, dz and phy) is done. With these coordinates the monomers are frozen but the interplanar distance, the displacements of the monomers along the X and Y axes and their mutual rotation are allowed. It works for G09 and the dimer remains bonded if a dispersion corrected method is used. Hope it helps! All the best! Vasile Mn N 1 1.9461950 C 2 1.3810384 1 125.9332101 N 3 1.3163169 2 127.4082075 1 0.0000000 C 4 1.3163169 3 123.3171647 2 0.0000000 N 5 1.3810384 4 127.4082075 3 0.0000000 C 6 1.3810384 5 108.1335798 4 180.0000000 N 7 1.3163169 6 127.4082075 5 180.0000000 C 8 1.3163169 7 123.3171647 6 0.0000000 N 9 1.3810384 8 127.4082075 7 0.0000000 C 10 1.3810384 9 108.1335798 8 180.0000000 N 11 1.3163169 10 127.4082075 9 180.0000000 C 12 1.3163169 11 123.3171647 10 0.0000000 N 13 1.3810384 12 127.4082075 11 0.0000000 C 14 1.3810384 13 108.1335798 12 180.0000000 N 15 1.3163169 14 127.4082075 13 180.0000000 C 16 1.3163169 15 123.3171647 14 0.0000000 C 3 1.4336424 2 108.8967427 1 180.0000000 C 18 1.3964000 3 107.0364674 2 0.0000000 C 19 1.3784863 18 121.4394707 3 180.0000000 C 20 1.3867360 19 117.1926090 18 0.0000000 C 21 1.3907500 20 121.3679203 19 0.0000000 C 18 1.3784863 3 131.5240619 2 180.0000000 C 5 1.4336424 4 123.6950497 3 180.0000000 C 24 1.3964000 5 107.0364674 4 180.0000000 C 25 1.3784863 24 121.4394707 5 180.0000000 C 26 1.3867360 25 117.1926090 24 0.0000000 C 27 1.3907500 26 121.3679203 25 0.0000000 C 24 1.3784863 5 131.5240619 4 0.0000000 C 11 1.4336424 10 108.8967427 9 0.0000000 C 30 1.3964000 11 107.0364674 10 0.0000000 C 31 1.3784863 30 121.4394707 11 180.0000000 C 32 1.3867360 31 117.1926090 30 0.0000000 C 33 1.3907500 32 121.3679203 31 0.0000000 C 30 1.3784863 11 131.5240619 10 180.0000000 C 13 1.4336424 12 123.6950497 11 180.0000000 C 36 1.3964000 13 107.0364674 12 180.0000000 C 37 1.3784863 36 121.4394707 13 180.0000000 C 38 1.3867360 37 117.1926090 36 0.0000000 C 39 1.3907500 38 121.3679203 37 0.0000000 C 36 1.3784863 13 131.5240619 12 0.0000000 H 20 1.0807847 19 121.1963519 18 180.0000000 H 21 1.0813335 20 119.4378468 19 180.0000000 H 22 1.0813335 21 119.1942328 20 180.0000000 H 23 1.0807847 18 121.1963519 3 0.0000000 H 26 1.0807847 25 121.1963519 24 180.0000000 H 27 1.0813335 26 119.4378468 25 180.0000000 H 28 1.0813335 27 119.1942328 26 180.0000000 H 29 1.0807847 24 121.1963519 5 0.0000000 H 32 1.0807847 31 121.1963519 30 180.0000000 H 33 1.0813335 32 119.4378468 31 180.0000000 H 34 1.0813335 33 119.1942328 32 180.0000000 H 35 1.0807847 30 121.1963519 11 0.0000000 H 41 1.0807847 36 121.1963519 13 0.0000000 H 40 1.0813335 39 119.1942328 38 180.0000000 H 39 1.0813335 38 119.4378468 37 180.0000000 H 38 1.0807847 37 121.1963519 36 180.0000000 X 1 1.0000000 2 90.0000000 17 -90.0000000 X 58 dz 3 108.5803374 4 88.2679521 X 59 dx 58 90.0000000 10 phy X 60 dy 59 90.0000000 58 90.0000000 Mn 61 2.4494897 60 65.9051574 59 63.4349488 N 62 1.9461950 61 65.9051566 60 180.00 C 63 1.3810384 62 125.9332101 61 -63.4349485 N 64 1.3163169 63 127.4082075 62 0.0000000 C 65 1.3163169 64 123.3171647 63 0.0000000 N 66 1.3810384 65 127.4082075 64 0.0000000 C 67 1.3810384 66 108.1335798 65 180.0000000 N 68 1.3163169 67 127.4082075 66 180.0000000 C 69 1.3163169 68 123.3171647 67 0.0000000 N 70 1.3810384 69 127.4082075 68 0.0000000 C 71 1.3810384 70 108.1335798 69 180.0000000 N 72 1.3163169 71 127.4082075 70 180.0000000 C 73 1.3163169 72 123.3171647 71 0.0000000 N 74 1.3810384 73 127.4082075 72 0.0000000 C 75 1.3810384 74 108.1335798 73 180.0000000 N 76 1.3163169 75 127.4082075 74 180.0000000 C 77 1.3163169 76 123.3171647 75 0.0000000 C 64 1.4336424 63 108.8967427 62 180.0000000 C 79 1.3964000 64 107.0364674 63 0.0000000 C 80 1.3784863 79 121.4394707 64 180.0000000 C 81 1.3867360 80 117.1926090 79 0.0000000 C 82 1.3907500 81 121.3679203 80 0.0000000 C 79 1.3784863 64 131.5240619 63 -180.0000000 C 66 1.4336424 65 123.6950497 64 -180.0000000 C 85 1.3964000 66 107.0364674 65 180.0000000 C 86 1.3784863 85 121.4394707 66 180.0000000 C 87 1.3867360 86 117.1926090 85 0.0000000 C 88 1.3907500 87 121.3679203 86 0.0000000 C 85 1.3784863 66 131.5240619 65 0.0000000 C 72 1.4336424 71 108.8967427 70 0.0000000 C 91 1.3964000 72 107.0364674 71 0.0000000 C 92 1.3784863 91 121.4394707 72 180.0000000 C 93 1.3867360 92 117.1926090 91 0.0000000 C 94 1.3907500 93 121.3679203 92 0.0000000 C 91 1.3784863 72 131.5240619 71 180.0000000 C 74 1.4336424 73 123.6950497 72 180.0000000 C 97 1.3964000 74 107.0364674 73 180.0000000 C 98 1.3784863 97 121.4394707 74 180.0000000 C 99 1.3867360 98 117.1926090 97 0.0000000 C 100 1.3907500 99 121.3679203 98 0.0000000 C 97 1.3784863 74 131.5240619 73 0.0000000 H 81 1.0807847 80 121.1963519 79 -180.0000000 H 82 1.0813335 81 119.4378468 80 -180.0000000 H 83 1.0813335 82 119.1942328 81 180.0000000 H 84 1.0807847 79 121.1963519 64 0.0000000 H 87 1.0807847 86 121.1963519 85 180.0000000 H 88 1.0813335 87 119.4378468 86 -180.0000000 H 89 1.0813335 88 119.1942328 87 180.0000000 H 90 1.0807847 85 121.1963519 66 0.0000000 H 93 1.0807847 92 121.1963519 91 180.0000000 H 94 1.0813335 93 119.4378468 92 180.0000000 H 95 1.0813335 94 119.1942328 93 180.0000000 H 96 1.0807847 91 121.1963519 72 0.0000000 H 102 1.0807847 97 121.1963519 74 0.0000000 H 101 1.0813335 100 119.1942328 99 180.0000000 H 100 1.0813335 99 119.4378468 98 180.0000000 H 99 1.0807847 98 121.1963519 97 180.0000000 variables: dx=1.2 dy=1.2 dz=0.5 phy=100.000000 On Wed, Mar 20, 2013 at 4:42 PM, Daniel Fernando Coimbra danielfcoimbra**gmail.com wrote: > > Sent to CCL by: Daniel Fernando Coimbra [danielfcoimbra],[gmail.com] > ORCA can easily do this. You can define two fragments and specify that thei > are constrained but that their "connection" is to be optimized. > You define each atoms fragment number by putting "(1)" or "(2)" at the > coords, after the atom, and use the likes of "ConnectFragments {1 2 C 12 > 28}" and "invertConstraints true" (this will optimize the connection between > fragments 1 and 2, connected by atoms 12 and 28, freezing everything else) > as detailed in the manual. > > Em 20/03/2013 01:27, Geoffrey Hutchison geoffh~~pitt.edu escreveu: > >> >> Sent to CCL by: Geoffrey Hutchison [geoffh]^[pitt.edu] >> I have a bit of a strange request. I'm looking to do a geometry >> optimization between two "frozen" molecular fragments. I'm using Gaussian, >> but any other modern DFT program would be fine. >> >> Consider, for example, optimizing benzene dimer. There are multiple local >> minima. And yes, the benzene geometry relaxes. But I mainly want to optimize >> the intermolecular distances and angles (i.e., 6 degrees of freedom). >> >> In principal, you should be able to do this with Gaussian's ModRedundant, >> but the obvious constraints haven't worked. I tried freezing with wildcards >> and *everything* was frozen. Since there are two benzenes, I don't really >> want to list 36 constraints if I can avoid it. (Yes, if all else fails, I'll >> write a script to generate the appropriate constraints. But this seems like >> a useful thing to ask for posterity.) >> >> Any creative ideas (or alternate programs)? >> >> Thanks very much, >> -Geoff >> >> --- >> Prof. Geoffrey Hutchison >> Department of Chemistry >> University of Pittsburgh >> tel: (412) 648-0492 >> email: geoffh()pitt.edu >> web: http://hutchison.chem.pitt.edu/ > > > -- > Daniel Fernando Coimbra > Grupo de Estrutura Eletrônica Molecular > Departamento de Química > Universidade Federal de Santa Catarinahttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > ====================== Prof.dr. Vasile Chis Babeş-Bolyai University Faculty of Physics Kogalniceanu 1 RO-400084 Cluj-Napoca Romania Tel: +40264405300 Fax: +40591906 vasile.chis]=[phys.ubbcluj.ro www.phys.ubbcluj.ro/~vasile.chis www.phys.ubbcluj.ro/seta ====================== From owner-chemistry@ccl.net Wed Mar 20 22:35:01 2013 From: "mehedi mehedi.acct_-_gmail.com" To: CCL Subject: CCL:G: Running crystal Structure Message-Id: <-48447-130320185654-5669-OANW68yUcmxBgEcS8ZT1Uw..server.ccl.net> X-Original-From: mehedi Content-Type: multipart/alternative; boundary=047d7b2edf0507dc4b04d86323c6 Date: Wed, 20 Mar 2013 17:56:47 -0500 MIME-Version: 1.0 Sent to CCL by: mehedi [mehedi.acct()gmail.com] --047d7b2edf0507dc4b04d86323c6 Content-Type: text/plain; charset=ISO-8859-1 Well, how do I know from the PBC output file that the reaction will occur? On Wed, Mar 20, 2013 at 3:37 PM, Susi Lehtola susi.lehtola~~ alumni.helsinki.fi wrote: > > Sent to CCL by: Susi Lehtola [susi.lehtola**alumni.helsinki.fi] > On Wed, 20 Mar 2013 13:47:07 -0400 > "Mehe H Khan mehedi.acct ~ gmail.com" wrote: > > > > > Sent to CCL by: "Mehe H Khan" [mehedi.acct * gmail.com] > > Hello, > > I want to work with a reaction. one of the reactants is in crystal > > structure. But as far as i know gaussian works with gas phase. Is > > there any way that I can work with crystal structure in gaussian? > > It can do periodic calculations (infinite system) as well > > http://www.gaussian.com/g_tech/g_ur/k_pbc.htm > -- > --------------------------------------------------------------- > Mr. Susi Lehtola, PhD Postdoctoral researcher > susi.lehtola%x%alumni.helsinki.fi Department of Applied Physics > http://www.helsinki.fi/~jzlehtol Aalto university > Finland > --------------------------------------------------------------- > Susi Lehtola, FT Tutkijatohtori > susi.lehtola%x%alumni.helsinki.fi Fysiikan laitos > http://www.helsinki.fi/~jzlehtol Aalto-yliopisto > ---------------------------------------------------------------> > > -- Md. Mehedi Hasan Khan PhD Research Assistant Computational Chemistry Laboratory Jackson State University Jackson, MS, USA --047d7b2edf0507dc4b04d86323c6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Well, how do I know from the PBC output file that the reaction will occur?<= br>
On Wed, Mar 20, 2013 at 3:37 PM, Susi Leh= tola susi.lehtola~~alumni.helsinki.fi= <owner-chemistry-.-ccl.net> wrote:

Sent to CCL by: Susi Lehtola [susi.lehtola**alumni.helsinki.fi]
On Wed, 20 Mar 2013 13:47:07 -0400
"Mehe H Khan mehedi.acct ~ gmail.com" <owner-chemistry%x%ccl.net> wrote:

>
> Sent to CCL by: "Mehe H Khan" [mehedi.acct * gmail.com]
> Hello,
> I want to work with a reaction. one of the reactants is in crystal
> structure. But as far as i know gaussian works with gas phase. Is
> there any way that I can work with crystal structure in gaussian?

It can do periodic calculations (infinite system) as well

http://www.gaussian.com/g_tech/g_ur/k_pbc.htm
--
---------------------------------------------------------------
Mr. Susi Lehtola, PhD =A0 =A0 =A0 =A0 =A0 =A0 Postdoctoral researcher
susi.lehtola%x%alum= ni.helsinki.fi =A0 Department of Applied Physics
http://www.h= elsinki.fi/~jzlehtol =A0Aalto university
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Finland=
---------------------------------------------------------------
Susi Lehtola, FT =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Tutkijatohtori
susi.lehtola%x%alum= ni.helsinki.fi =A0 Fysiikan laitos
http://www.h= elsinki.fi/~jzlehtol =A0Aalto-yliopisto
---------------------------------------------------------------



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--
=
Md. Mehedi Hasan Khan
PhD Research Assistant
Compu= tational Chemistry Laboratory
Jackson State University
Jackson, MS, USA
--047d7b2edf0507dc4b04d86323c6--