From owner-chemistry@ccl.net Wed Nov 21 00:47:00 2007 From: "Markus Thut markus.thut..iac.unibe.ch" To: CCL Subject: CCL:G: AW: G: AW: CIS Optimization for the First Singlet Excited State Message-Id: <-35664-071120115427-18236-Njo/6XoxRiYG9oO2LQCSqw]~[server.ccl.net> X-Original-From: "Markus Thut" Content-Type: multipart/alternative; boundary="----=_NextPart_000_001C_01C82B9E.55153720" Date: Tue, 20 Nov 2007 17:54:00 +0100 MIME-Version: 1.0 Sent to CCL by: "Markus Thut" [markus.thut::iac.unibe.ch] This is a multi-part message in MIME format. ------=_NextPart_000_001C_01C82B9E.55153720 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Sue =20 It is certainly true that this mixing of the LUMO and LUMO+1 is the = problem causing the mixing of the two transitions. Usually such mixings occur at transition states. Is it a transition state or just a local minima? =20 The systems we observed such interchanges are _not_ symmetric either. = Thus, we forced them to be. Maybe you are able to do something similar. =20 The _calcall_ calculates the forces at each point in the optimization. = Thus, the minimization algorithm can easily step into the direction of the = largest force contribution. This speeds up convergence (or makes it possible for shallow potentials), but strongly slows down your calculations. So use = it just in case you have convergence problems. =20 Cheers =20 Markus =20 =20 _____ =20 Von: owner-chemistry_+_ccl.net [mailto:owner-chemistry_+_ccl.net]=20 Gesendet: Dienstag, 20. November 2007 04:04 An: Thut, Markus Betreff: CCL:G: AW: CIS Optimization for the First Singlet Excited State =20 Dear Markus Thank you very much for your suggestion.=20 =20 The compound that I have studied do not have any symmetry. In my case, = the LUMO and LUMO+1 is mixed. That might caused the problem for the = interchange of the excited states. =20 The basis set that I used is 6-31g* for all atoms. Is the optimization = more easiler to get converged with Calcall keyword? =20 Best regards, Sue =20 "Markus Thut markus.thut[-]iac.unibe.ch" = wrote: Sent to CCL by: "Markus Thut" [markus.thut+/-iac.unibe.ch] Dear Sue We usedd to encounter this problem too. What we found is that i) upon interchange of the excited states, the electronic character of = the two states interchange. Thus, a "major" change in geometry occurs upon = this change. Please check the evolution of your optimized molecule. ii) Usually, such interchanges occur due to symmetry-breaking = optimization steps. Sometimes, you can prevent interchanges by restricting the optimization to e.g. Cs instead of C1, even though the cluster/molecule = you are optimizing is presumably C1. iii) if you have a symmetry wich allows optimizations for a' or a" transitions, try to optimize for the desired transition (you can do this = in TURBOMOLE, I'm not sure about Gaussian03). In this case, you should get = a minima for the a' and on for the a" transition. Comparing these two geometries, you should find the structural change responsible for the interchange of the two states. We found, for example thath for hydroxyquinolines, such an interchage is induced by a significant change = of the angle of the quinone-N. iv) there might be some problems with your basis set (inducing = structural changes and so on), maybe you first choose a standard basis set? v) try the CalcAll parameter for the opt command. Cheers, Markus > -----Urspr=FCngliche Nachricht----- > Von: owner-chemistry .. ccl.net [mailto:owner-chemistry .. ccl.net] > Gesendet: Samstag, 17. November 2007 03:05 > An: Thut, Markus > Betreff: CCL: CIS Optimization for the First Singlet Excited State >=20 >=20 > Sent to CCL by: "Sue L" [chsue2004 ~~ yahoo.com] > Hi all, >=20 > I have performed a CIS optimization for the first singlet excited = state > with the keywords #n cis(root=3D1,direct) gen opt >=20 > However, the optimization cannot be converged. I found that in the = middle > of the optimization, the first- and second- excited state swapped, as > indicated in the section of Excitation energies and oscillator = strength > (as below). >=20 > --------- > Excited State 1: Singlet-A 3.7320 eV 332.22 nm f=3D0.1634 > 93 -> 94 0.67286 > This state for optimization and/or second-order correction. > Copying the excited state density for this state as the 1-particle = RhoCI > density. >=20 > Excited State 2: Singlet-A 5.5654 eV 222.78 nm f=3D0.2648 > 91 -> 94 -0.12140 > 91 -> 96 -0.14274 > 92 -> 94 0.46889 > 92 -> 95 -0.14756 > 93 -> 95 -0.35249 > --------- >=20 > --------- > Excited State 1: Singlet-A 5.5227 eV 224.50 nm f=3D0.2035 > 91 -> 94 -0.11890 > 91 -> 95 -0.11553 > 91 -> 96 -0.13341 > 92 -> 94 0.46589 > 92 -> 95 -0.17450 > 93 -> 95 -0.35340 > This state for optimization and/or second-order correction. > Copying the excited state density for this state as the 1-particle = RhoCI > density. >=20 > Excited State 2: Singlet-A 4.0937 eV 302.86 nm f=3D0.1943 > 92 -> 95 -0.11059 > 93 -> 94 0.66385 > -------- >=20 > Could anyone know what the problem is? >=20 > Thank you very much. >=20 > Sue >=20 >=20 >=20 > >> > > > > > >=20 > > > >=20 > =3D>=20 >=20 your = homepage. ------=_NextPart_000_001C_01C82B9E.55153720 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear = Sue

 =

It is certainly = true that this mixing of the LUMO and LUMO+1 is the problem causing the mixing of = the two transitions. Usually such mixings occur at transition states. Is it a transition state or just a local minima?

 =

The systems we = observed such interchanges are _not_ symmetric either. Thus, we forced them to be. Maybe you are able to do something similar.

 =

The _calcall_ calculates the forces at = each point in the optimization. Thus, the minimization algorithm can easily = step into the direction of the largest force contribution. This speeds up convergence (or makes it possible for shallow potentials), but strongly = slows down your calculations. So use it just in case you have convergence = problems.

 =

=A0Cheers

 =

Markus

 

=

 =

Von: owner-chemistry_+_ccl.net [mailto:owner-chemistry_+_ccl.net]
Gesendet: Dienstag, 20. = November 2007 04:04
An: Thut, Markus =
Betreff: CCL:G: AW: CIS Optimization for the First Singlet Excited = State

 

Dear Markus

Thank you very much for your suggestion. =

 

The compound that I have studied do not have any = symmetry. In my case, the LUMO and LUMO+1 is mixed. That might caused the problem = for the interchange of the excited states.

 

The basis set that I used is 6-31g* for all atoms. Is the = optimization more easiler to get converged with Calcall keyword?

 

Best regards,

Sue

 



"Markus = Thut markus.thut[-]iac.unibe.ch" = <owner-chemistry|-|ccl.net> wrote:


Sent to CCL by: "Markus Thut" [markus.thut+/-iac.unibe.ch]
Dear Sue

We usedd to encounter this problem too. What we found is that

i) upon interchange of the excited states, the electronic character of = the
two states interchange. Thus, a "major" change in geometry = occurs upon this
change. Please check the evolution of your optimized molecule.

ii) Usually, such interchanges occur due to symmetry-breaking = optimization
steps. Sometimes, you can prevent interchanges by restricting the
optimization to e.g. Cs instead of C1, even though the cluster/molecule = you
are optimizing is presumably C1.

iii) if you have a symmetry wich allows optimizations for a' or = a"
transitions, try to optimize for the desired transition (you can do this = in
TURBOMOLE, I'm not sure about Gaussian03). In this case, you should get = a
minima for the a' and on for the a" transition. Comparing these = two
geometries, you should find the structural change responsible for = the
interchange of the two states. We found, for example thath for
hydroxyquinolines, such an interchage is induced by a significant change = of
the angle of the quinone-N.

iv) there might be some problems with your basis set (inducing = structural
changes and so on), maybe you first choose a standard basis set?

v) try the CalcAll parameter for the opt command.

Cheers,

Markus


> -----Urspr=FCngliche Nachricht-----
> Von: owner-chemistry .. ccl.net [mailto:owner-chemistry .. = ccl.net]
> Gesendet: Samstag, 17. November 2007 03:05
> An: Thut, Markus
> Betreff: CCL: CIS Optimization for the First Singlet Excited = State
>
>
> Sent to CCL by: "Sue L" [chsue2004 ~~ yahoo.com]
> Hi all,
>
> I have performed a CIS optimization for the first singlet excited = state
> with the keywords #n cis(root=3D1,direct) gen opt
>
> However, the optimization cannot be converged. I found that in the = middle
> of the optimization, the first- and second- excited state swapped, = as
> indicated in the section of Excitation energies and oscillator = strength
> (as below).
>
> ---------
> Excited State 1: Singlet-A 3.7320 eV 332.22 nm f=3D0.1634
> 93 -> 94 0.67286
> This state for optimization and/or second-order correction.
> Copying the excited state density for this state as the 1-particle = RhoCI
> density.
>
> Excited State 2: Singlet-A 5.5654 eV 222.78 nm f=3D0.2648
> 91 -> 94 -0.12140
> 91 -> 96 -0.14274
> 92 -> 94 0.46889
> 92 -> 95 -0.14756
> 93 -> 95 -0.35249
> ---------
>
> ---------
> Excited State 1: Singlet-A 5.5227 eV 224.50 nm f=3D0.2035
> 91 -> 94 -0.11890
> 91 -> 95 -0.11553
> 91 -> 96 -0.13341
> 92 -> 94 0.46589
> 92 -> 95 -0.17450
> 93 -> 95 -0.35340
> This state for optimization and/or second-order correction.
> Copying the excited state density for this state as the 1-particle = RhoCI
> density.
>
> Excited State 2: Singlet-A 4.0937 eV 302.86 nm f=3D0.1943
> 92 -> 95 -0.11059
> 93 -> 94 0.66385
> --------
>
> Could anyone know what the problem is?
>
> Thank you very much.
>
> Sue
>
>
>
>
>> > > > > >
>
>
> > >
> =3D>
>


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<BR
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<BR


 

=A0

Never miss a thing. Mak= e Yahoo your homepage.

------=_NextPart_000_001C_01C82B9E.55153720-- From owner-chemistry@ccl.net Wed Nov 21 01:51:01 2007 From: "Wenrui Zheng wenruizheng{:}gmail.com" To: CCL Subject: CCL: How to ensure the most stable configuration? Message-Id: <-35665-071121014904-13563-quo7FZ6FaL50Sd0rrjeG4Q ~~ server.ccl.net> X-Original-From: "Wenrui Zheng" Date: Wed, 21 Nov 2007 01:49:00 -0500 Sent to CCL by: "Wenrui Zheng" [wenruizheng[-]gmail.com] Dear, How should I find the most stable configuration among various configurations of a molecule? To compare their electronic energies, Gibbs free energies in gas, or Gibbs free energies in gas plus solvent energies? In some instances, the configuration with lowest Gibbs free energies in gas is not the most stable one in solvent. Because the reaction is carried out in aqueous solvent, the solvent effect couldn't be neglected. Another problem is the veracity of solvent energies. Different solvent models give different values. Regards, Wenrui Zheng From owner-chemistry@ccl.net Wed Nov 21 04:34:01 2007 From: "Laxmikanth Rao Joshi lkjoshiji!=!yahoo.com" To: CCL Subject: CCL: constructing polymer from repeating units Message-Id: <-35666-071121042929-8680-steYR7b9dvBMAW9QR5Mn3g[*]server.ccl.net> X-Original-From: "Laxmikanth Rao Joshi" Date: Wed, 21 Nov 2007 04:29:25 -0500 Sent to CCL by: "Laxmikanth Rao Joshi" [lkjoshiji],[yahoo.com] Hi to all Please I want to know any (free)software for constructing polymer strcuture from its repeating unit. Thanks in advance Joshi From owner-chemistry@ccl.net Wed Nov 21 05:46:00 2007 From: "Hemant Srivastava hemantkrsri..gmail.com" To: CCL Subject: CCL:G: IRC calculation Message-Id: <-35667-071121043852-11024-CppTkjxVkPjXbJ0+0eMTIg_+_server.ccl.net> X-Original-From: "Hemant Srivastava" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 21 Nov 2007 11:09:26 +0200 MIME-Version: 1.0 Sent to CCL by: "Hemant Srivastava" [hemantkrsri a gmail.com] Hi Alex, I think you can try reverse IRC calculation and if you are getting again opposite result its fine. Also you dont need to use CALCFC if you are reading geometry from chk file of frequency calculation. You can use RCFC instead of CALCFC for all type of IRC calculation, because it can read the same force constant from the chk file. If you want to use CALCALL its fine but only if RCFC is not working. Hope it will help you. Hemant ============================== Dr. Hemant Kumar Srivastava, Postdoctoral Fellow, Department of Medicinal Chemistry and Natural Products, School of Pharmacy, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, Jerusalem - 91120, ISRAEL, Phone- +972-2-6757495, Fax- 972-2-6757076, Cell- +972-546582016, ========================================================== > > From: "Alexander Hoepker achoepker-.-gmail.com" > Date: Tuesday, November 20, 2007 11:59 am > Subject: CCL:G: IRC calculation > To: "Kamerlin, Shina " > > > > > Sent to CCL by: "Alexander Hoepker" [achoepker.:.gmail.com] > > I'm performing a forward IRC calculation starting with a transition > > state that has been optimized in Gaussian 03 in B3LYP (6/31G(d)) level > > of theory. The transition state was verified by one imaginary > > frequency for this particular deprotonation. > > > > my keywords are: #T B3LYP/6-31G(d) IRC=(CalcFC,Forward,MaxPoints=40) > > > > After only a couple of points the IRC appears to search backwards > > instead of forwards. IRC calculations are black magic for me and to be > > honest it is not surprising to me that the program confused the > > backward with the forward reaction coordinate. Could someone give > > me a > > hint as what I might be doing wrong or how I could tip the calculation > > in the right direction. Thanks a lot in advance. > > > > Alex > > > > > > > > -= This is automatically added to each message by the mailing > > script =- > > To recover the email address of the author of the message, please > > changethe strange characters on the top line to the ,, sign. You can > > also> Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > +-+-+> > > > From owner-chemistry@ccl.net Wed Nov 21 05:58:00 2007 From: "Sue Lam chsue2004_._yahoo.com" To: CCL Subject: CCL:G: AW: G: AW: CIS Optimization for the First Singlet Excited State Message-Id: <-35668-071121055317-9963-ewP6+t5sa4wd4z+6VdIvMg!=!server.ccl.net> X-Original-From: Sue Lam Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1194360569-1195638784=:45847" Date: Wed, 21 Nov 2007 01:53:04 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004%a%yahoo.com] --0-1194360569-1195638784=:45847 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Markus, It is a local minimum. After you found the excited state with symmetry constraint, did you reoptimize your system into a C1 symmtery? Thanks, Sue "Markus Thut markus.thut..iac.unibe.ch" wrote: v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} Dear Sue It is certainly true that this mixing of the LUMO and LUMO+1 is the problem causing the mixing of the two transitions. Usually such mixings occur at transition states. Is it a transition state or just a local minima? The systems we observed such interchanges are _not_ symmetric either. Thus, we forced them to be. Maybe you are able to do something similar. The _calcall_ calculates the forces at each point in the optimization. Thus, the minimization algorithm can easily step into the direction of the largest force contribution. This speeds up convergence (or makes it possible for shallow potentials), but strongly slows down your calculations. So use it just in case you have convergence problems.  Cheers Markus --------------------------------- Von: owner-chemistry[A]ccl.net [mailto:owner-chemistry[A]ccl.net] Gesendet: Dienstag, 20. November 2007 04:04 An: Thut, Markus Betreff: CCL:G: AW: CIS Optimization for the First Singlet Excited State Dear Markus Thank you very much for your suggestion. The compound that I have studied do not have any symmetry. In my case, the LUMO and LUMO+1 is mixed. That might caused the problem for the interchange of the excited states. The basis set that I used is 6-31g* for all atoms. Is the optimization more easiler to get converged with Calcall keyword? Best regards, Sue "Markus Thut markus.thut[-]iac.unibe.ch" wrote: Sent to CCL by: "Markus Thut" [markus.thut+/-iac.unibe.ch] Dear Sue We usedd to encounter this problem too. What we found is that i) upon interchange of the excited states, the electronic character of the two states interchange. Thus, a "major" change in geometry occurs upon this change. Please check the evolution of your optimized molecule. ii) Usually, such interchanges occur due to symmetry-breaking optimization steps. Sometimes, you can prevent interchanges by restricting the optimization to e.g. Cs instead of C1, even though the cluster/molecule you are optimizing is presumably C1. iii) if you have a symmetry wich allows optimizations for a' or a" transitions, try to optimize for the desired transition (you can do this in TURBOMOLE, I'm not sure about Gaussian03). In this case, you should get a minima for the a' and on for the a" transition. Comparing these two geometries, you should find the structural change responsible for the interchange of the two states. We found, for example thath for hydroxyquinolines, such an interchage is induced by a significant change of the angle of the quinone-N. iv) there might be some problems with your basis set (inducing structural changes and so on), maybe you first choose a standard basis set? v) try the CalcAll parameter for the opt command. Cheers, Markus > -----Ursprüngliche Nachricht----- > Von: owner-chemistry .. ccl.net [mailto:owner-chemistry .. ccl.net] > Gesendet: Samstag, 17. November 2007 03:05 > An: Thut, Markus > Betreff: CCL: CIS Optimization for the First Singlet Excited State > > > Sent to CCL by: "Sue L" [chsue2004 ~~ yahoo.com] > Hi all, > > I have performed a CIS optimization for the first singlet excited state > with the keywords #n cis(root=1,direct) gen opt > > However, the optimization cannot be converged. I found that in the middle > of the optimization, the first- and second- excited state swapped, as > indicated in the section of Excitation energies and oscillator strength > (as below). > > --------- > Excited State 1: Singlet-A 3.7320 eV 332.22 nm f=0.1634 > 93 -> 94 0.67286 > This state for optimization and/or second-order correction. > Copying the excited state density for this state as the 1-particle RhoCI > density. > > Excited State 2: Singlet-A 5.5654 eV 222.78 nm f=0.2648 > 91 -> 94 -0.12140 > 91 -> 96 -0.14274 > 92 -> 94 0.46889 > 92 -> 95 -0.14756 > 93 -> 95 -0.35249 > --------- > > --------- > Excited State 1: Singlet-A 5.5227 eV 224.50 nm f=0.2035 > 91 -> 94 -0.11890 > 91 -> 95 -0.11553 > 91 -> 96 -0.13341 > 92 -> 94 0.46589 > 92 -> 95 -0.17450 > 93 -> 95 -0.35340 > This state for optimization and/or second-order correction. > Copying the excited state density for this state as the 1-particle RhoCI > density. > > Excited State 2: Singlet-A 4.0937 eV 302.86 nm f=0.1943 > 92 -> 95 -0.11059 > 93 -> 94 0.66385 > -------- > > Could anyone know what the problem is? > > Thank you very much. > > Sue > > > > >> > > > > > > > > > > > => > Dear Markus,
 
It is a local minimum.
 
After you found the excited state with symmetry constraint, did you reoptimize your system into a C1 symmtery?
 
Thanks,
Sue

"Markus Thut markus.thut..iac.unibe.ch" <owner-chemistry a ccl.net> wrote:
Dear Sue
 
It is certainly true that this mixing of the LUMO and LUMO+1 is the problem causing the mixing of the two transitions. Usually such mixings occur at transition states. Is it a transition state or just a local minima?
 
The systems we observed such interchanges are _not_ symmetric either. Thus, we forced them to be. Maybe you are able to do something similar.
 
The _calcall_ calculates the forces at each point in the optimization. Thus, the minimization algorithm can easily step into the direction of the largest force contribution. This speeds up convergence (or makes it possible for shallow potentials), but strongly slows down your calculations. So use it just in case you have convergence problems.
 
 Cheers
 
Markus
 
 
Von: owner-chemistry[A]ccl.net [mailto:owner-chemistry[A]ccl.net]
Gesendet: Dienstag, 20. November 2007 04:04
An: Thut, Markus
Betreff: CCL:G: AW: CIS Optimization for the First Singlet Excited State
 
Dear Markus
Thank you very much for your suggestion.
 
The compound that I have studied do not have any symmetry. In my case, the LUMO and LUMO+1 is mixed. That might caused the problem for the interchange of the excited states.
 
The basis set that I used is 6-31g* for all atoms. Is the optimization more easiler to get converged with Calcall keyword?
 
Best regards,
Sue
 


"Markus Thut markus.thut[-]iac.unibe.ch" <owner-chemistry|-|ccl.net> wrote:

Sent to CCL by: "Markus Thut" [markus.thut+/-iac.unibe.ch]
Dear Sue

We usedd to encounter this problem too. What we found is that

i) upon interchange of the excited states, the electronic character of the
two states interchange. Thus, a "major" change in geometry occurs upon this
change. Please check the evolution of your optimized molecule.

ii) Usually, such interchanges occur due to symmetry-breaking optimization
steps. Sometimes, you can prevent interchanges by restricting the
optimization to e.g. Cs instead of C1, even though the cluster/molecule you
are optimizing is presumably C1.

iii) if you have a symmetry wich allows optimizations for a' or a"
transitions, try to optimize for the desired transition (you can do this in
TURBOMOLE, I'm not sure about Gaussian03). In this case, you should get a
minima for the a' and on for the a" transition. Comparing these two
geometries, you should find the structural change responsible for the
interchange of the two states. We found, for example thath for
hydroxyquinolines, such an interchage is induced by a significant change of
the angle of the quinone-N.

iv) there might be some problems with your basis set (inducing structural
changes and so on), maybe you first choose a standard basis set?

v) try the CalcAll parameter for the opt command.

Cheers,

Markus


> -----Ursprüngliche Nachricht-----
> Von: owner-chemistry .. ccl.net [mailto:owner-chemistry .. ccl.net]
> Gesendet: Samstag, 17. November 2007 03:05
> An: Thut, Markus
> Betreff: CCL: CIS Optimization for the First Singlet Excited State
>
>
> Sent to CCL by: "Sue L" [chsue2004 ~~ yahoo.com]
> Hi all,
>
> I have performed a CIS optimization for the first singlet excited state
> with the keywords #n cis(root=1,direct) gen opt
>
> However, the optimization cannot be converged. I found that in the middle
> of the optimization, the first- and second- excited state swapped, as
> indicated in the section of Excitation energies and oscillator strength
> (as below).
>
> ---------
> Excited State 1: Singlet-A 3.7320 eV 332.22 nm f=0.1634
> 93 -> 94 0.67286
> This state for optimization and/or second-order correction.
> Copying the excited state density for this state as the 1-particle RhoCI
> density.
>
> Excited State 2: Singlet-A 5.5654 eV 222.78 nm f=0.2648
> 91 -> 94 -0.12140
> 91 -> 96 -0.14274
> 92 -> 94 0.46889
> 92 -> 95 -0.14756
> 93 -> 95 -0.35249
> ---------
>
> ---------
> Excited State 1: Singlet-A 5.5227 eV 224.50 nm f=0.2035
> 91 -> 94 -0.11890
> 91 -> 95 -0.11553
> 91 -> 96 -0.13341
> 92 -> 94 0.46589
> 92 -> 95 -0.17450
> 93 -> 95 -0.35340
> This state for optimization and/or second-order correction.
> Copying the excited state density for this state as the 1-particle RhoCI
> density.
>
> Excited State 2: Singlet-A 4.0937 eV 302.86 nm f=0.1943
> 92 -> 95 -0.11059
> 93 -> 94 0.66385
> --------
>
> Could anyone know what the problem is?
>
> Thank you very much.
>
> Sue
>
>
>
>
>> > > > > >
>
>
> > >
> =>
>


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?
Never miss a thing. Make Yahoo your homepage.

Never miss a thing. Make Yahoo your homepage. --0-1194360569-1195638784=:45847-- From owner-chemistry@ccl.net Wed Nov 21 06:49:01 2007 From: "Lukasz Cwiklik cwiklik||gmail.com" To: CCL Subject: CCL: Intel Quad-core vs AMD Opteron Message-Id: <-35669-071121060913-21823-SUS4YwTzjYDAT42n+ksySQ]^[server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 21 Nov 2007 12:13:21 +0200 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik|*|gmail.com] On Nov 21, 2007 4:14 AM, Hod Greeley hod-ccl===greeley.org wrote: > Sent to CCL by: "Hod Greeley" [hod-ccl||greeley.org] > Hello, > > Regarding #2, there could be a few reasons why you would not expect the > processing power to scale linearly with the number of cores. There is a > lot more to a system than just the cpu. > Hi, Regarding the scaling, just like Hod said, this is not only the number of CPUs that matters. We have some experience with ab-initio MD (cp2k/quickstep) running on 2xOpteronDualCore (4 cores on each node), 8GB RAM per node, nodes connected via 10 Gigabit InfiniBand, running 64bit Debian. Jobs fit into RAM so disks are almost not used. In our case it is about 20% more efficient to spread one multiprocessor job between nodes that to calculate it on more than one core on each node. It is mostly, I think, due to CPU<->RAM bottlenecks and fast Ethernet . So, unless you test it, you are never sure what the real efficiency of your system will be :( Best, Lukasz Cwiklik -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Wed Nov 21 07:23:00 2007 From: "Arvydas Tamulis tamulis..mserv.itpa.lt" To: CCL Subject: CCL: [NWCHEM, CCL] again about BSSE: in system of 145 molecules Message-Id: <-35670-071121065102-23896-Kgag8lIxvL3+EqNaX/G/SA{=}server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: MULTIPART/MIXED; BOUNDARY="0-365816569-1195645833=:98940" Date: Wed, 21 Nov 2007 13:50:33 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis|mserv.itpa.lt] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. --0-365816569-1195645833=:98940 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE Dear Colleagues, My friends support to run my DFT tasks calculating=20 Guanine::Cytosine conformations in the=20 surrounding of real 143 solvent molecules, i.e. I have 145 molecules in=20 total in the supramolecular system. How to evaluate the BSSE in this case? Cheers, Arvydas On Wed, 21 Nov 2007, Maria Angels Carvajal wrote: > Dear all, > I'm trying to compute the BSSE for a molecule. For the whole complex, I > don=B4t have any problem, but when I change some of the atoms for Bqs, th= e > calculation didn=B4t finish fine. > I calculated BSSE for other molecules and using other basis sets and I ha= d > not any problem. I have this problem only in this case. > Does someone know how can I overcome this? Thanks, > --0-365816569-1195645833=:98940-- From owner-chemistry@ccl.net Wed Nov 21 07:58:01 2007 From: "Alessandro Contini alessandro.contini]~[unimi.it" To: CCL Subject: CCL: constructing polymer from repeating units Message-Id: <-35671-071121065153-24603-x0kS9c/TtOZFzZzfu5sQeg- -server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 7bit Content-type: text/plain Date: Wed, 21 Nov 2007 12:00:49 +0100 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini^-^unimi.it] Hi, I solved a similar issue by using VEGA ZZ http://www.ddl.unimi.it/vega/index2.htm You can build your main unit (or units, if you need tacticity), save it as a fragment and build PDB file structured in different residues (one for each unit). The following example is a small PVP trimer, where VPI is the first monomer and VP1 and VP2 are central units having different chirality. ATOM 1 C3 VPI 1 -5.797 -47.156 -10.227 1.00 0.00 ATOM 2 C2 VPI 1 -5.513 -46.833 -8.758 1.00 0.00 ATOM 3 C1 VPI 1 -6.645 -45.876 -8.430 1.00 0.00 ATOM 4 O VPI 1 -7.122 -45.643 -7.332 1.00 0.00 ATOM 5 C4 VPI 1 -6.266 -45.787 -10.737 1.00 0.00 ATOM 6 N VPI 1 -7.049 -45.308 -9.591 1.00 0.00 ATOM 7 CA VPI 1 -8.130 -44.321 -9.721 1.00 0.00 ATOM 8 HA2 VPI 1 -8.665 -44.523 -10.653 1.00 0.00 ATOM 9 HA1 VPI 1 -8.834 -44.446 -8.893 1.00 0.00 ATOM 10 CB VPI 1 -7.597 -42.871 -9.729 1.00 0.00 ATOM 11 HB2 VPI 1 -7.035 -42.700 -8.807 1.00 0.00 ATOM 12 HB1 VPI 1 -6.898 -42.739 -10.559 1.00 0.00 ATOM 13 H31 VPI 1 -6.583 -47.898 -10.320 1.00 0.00 ATOM 14 H32 VPI 1 -4.924 -47.525 -10.755 1.00 0.00 ATOM 15 H22 VPI 1 -4.569 -46.323 -8.603 1.00 0.00 ATOM 16 H21 VPI 1 -5.546 -47.698 -8.105 1.00 0.00 ATOM 17 H42 VPI 1 -5.443 -45.111 -10.937 1.00 0.00 ATOM 18 H41 VPI 1 -6.866 -45.853 -11.637 1.00 0.00 ATOM 19 C3 VP2 2 -11.084 -43.177 -12.365 1.00 0.00 ATOM 20 C2 VP2 2 -10.329 -42.167 -13.230 1.00 0.00 ATOM 21 C1 VP2 2 -9.165 -41.809 -12.324 1.00 0.00 ATOM 22 O VP2 2 -8.062 -41.424 -12.673 1.00 0.00 ATOM 23 C4 VP2 2 -10.945 -42.517 -10.992 1.00 0.00 ATOM 24 N VP2 2 -9.564 -42.017 -11.044 1.00 0.00 ATOM 25 CA VP2 2 -8.740 -41.832 -9.827 1.00 0.00 ATOM 26 HA2 VP2 2 -9.394 -42.021 -8.971 1.00 0.00 ATOM 27 CB VP2 2 -8.197 -40.388 -9.660 1.00 0.00 ATOM 28 HB2 VP2 2 -7.527 -40.346 -8.796 1.00 0.00 ATOM 29 HB1 VP2 2 -7.584 -40.133 -10.525 1.00 0.00 ATOM 30 H31 VP2 2 -10.603 -44.150 -12.386 1.00 0.00 ATOM 31 H32 VP2 2 -12.116 -43.304 -12.670 1.00 0.00 ATOM 32 H22 VP2 2 -10.897 -41.266 -13.441 1.00 0.00 ATOM 33 H21 VP2 2 -9.969 -42.572 -14.167 1.00 0.00 ATOM 34 H42 VP2 2 -11.639 -41.695 -10.862 1.00 0.00 ATOM 35 H41 VP2 2 -11.096 -43.209 -10.170 1.00 0.00 ATOM 36 C3 VP1 3 -9.904 -39.774 -5.832 1.00 0.00 ATOM 37 C2 VP1 3 -11.345 -39.845 -6.343 1.00 0.00 ATOM 38 C1 VP1 3 -11.128 -39.964 -7.841 1.00 0.00 ATOM 39 O VP1 3 -11.891 -40.457 -8.650 1.00 0.00 ATOM 40 C4 VP1 3 -9.268 -38.900 -6.916 1.00 0.00 ATOM 41 N VP1 3 -9.923 -39.415 -8.129 1.00 0.00 ATOM 42 CA VP1 3 -9.323 -39.335 -9.480 1.00 0.00 ATOM 43 HA1 VP1 3 -10.098 -39.554 -10.218 1.00 0.00 ATOM 44 CB VP1 3 -8.781 -37.914 -9.797 1.00 0.00 ATOM 45 HB2 VP1 3 -8.028 -37.646 -9.051 1.00 0.00 ATOM 46 HB1 VP1 3 -8.266 -37.923 -10.759 1.00 0.00 ATOM 47 H31 VP1 3 -9.449 -40.759 -5.803 1.00 0.00 ATOM 48 H32 VP1 3 -9.829 -39.340 -4.841 1.00 0.00 ATOM 49 H22 VP1 3 -11.919 -38.948 -6.142 1.00 0.00 ATOM 50 H21 VP1 3 -11.900 -40.700 -5.972 1.00 0.00 ATOM 51 H42 VP1 3 -9.491 -37.847 -6.786 1.00 0.00 ATOM 52 H41 VP1 3 -8.189 -39.003 -6.960 1.00 0.00 Hope this help Alessandro Il giorno mer, 21/11/2007 alle 04.29 -0500, Laxmikanth Rao Joshi lkjoshiji!=!yahoo.com ha scritto: > Sent to CCL by: "Laxmikanth Rao Joshi" [lkjoshiji],[yahoo.com] > > Hi to all > > Please I want to know any (free)software for constructing polymer strcuture from its repeating unit. > > Thanks in advance > > Joshi> > > -- Dr. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Universita' degli Studi di Milano, Facolta' di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini,unimi.it skype alessandrocontini From owner-chemistry@ccl.net Wed Nov 21 08:34:01 2007 From: "Jimmy Stewart MrMOPAC-.-att.net" To: CCL Subject: CCL: constructing polymer from repeating units Message-Id: <-35672-071121081847-21856-Phas3tJNPJ0oTVm364yr1Q|*|server.ccl.net> X-Original-From: Jimmy Stewart Content-Type: multipart/alternative; boundary="=====================_31981234==.ALT" Date: Wed, 21 Nov 2007 06:18:18 -0700 Mime-Version: 1.0 Sent to CCL by: Jimmy Stewart [MrMOPAC(_)att.net] --=====================_31981234==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Joshi asked, "Please I want to know any (free)software for constructing polymer strcuture from its repeating unit." The MOPAC2007 utility MAKPOL will construct a Cartesian data set for polymers, layer systems and solids, given the number of mers needed, a unit cell and the appropriate translation vectors. To download a Windows executable, please see: http://openmopac.net/manual/makpol.html Jimmy --=====================_31981234==.ALT Content-Type: text/html; charset="us-ascii"
Joshi asked, "Please I want to know any (free)software for constructing polymer strcuture from its repeating unit."

The MOPAC2007 utility MAKPOL will construct a Cartesian data set for polymers, layer systems and solids, given the number of mers needed, a unit cell and the appropriate translation vectors.

To download a Windows executable, please see:

http ://openmopac.net/manual/makpol.html

Jimmy
--=====================_31981234==.ALT-- From owner-chemistry@ccl.net Wed Nov 21 09:09:00 2007 From: "Chen Wang pleasant1789-,-gmail.com" To: CCL Subject: CCL: How to ensure the most stable configuration Message-Id: <-35673-071120224001-8789-r/QrF3YEqxwUle6vJ3GFsg=-=server.ccl.net> X-Original-From: "Chen Wang" Date: Tue, 20 Nov 2007 22:39:57 -0500 Sent to CCL by: "Chen Wang" [pleasant1789]_[gmail.com] How should I find the most stable configuration among various configurations of a molecule? To compare their electronic energies, Gibbs free energies in gas, or Gibbs free energies in gas plus solvent energies? In some instances, the configuration with lowest Gibbs free energies in gas is not the most stable one in solvent. Because the reaction is carried out in aqueous solvent, the solvent effect couldn't be neglected. Another problem is the veracity of solvent energies. Different solvent models give different values. Regards, Wang, Chen pleasant1789=gmail.com From owner-chemistry@ccl.net Wed Nov 21 09:44:01 2007 From: "Alain Alloche alain.allouche-*-univ-provence.fr" To: CCL Subject: CCL: crystal structure codes Message-Id: <-35674-071121025300-10329-YViMCDtad6ODvhgJynbLOQ : server.ccl.net> X-Original-From: "Alain Alloche" Date: Wed, 21 Nov 2007 02:52:56 -0500 Sent to CCL by: "Alain Alloche" [alain.allouche(-)univ-provence.fr] Dear CCLers, Do you know crystal cell manipulation codes other than Cerius2 ? doing crystal surface cleaving and surface cell building ? From owner-chemistry@ccl.net Wed Nov 21 10:19:00 2007 From: "Justin Finnerty justin.finnerty,uni-oldenburg.de" To: CCL Subject: CCL: IRC calculation Message-Id: <-35675-071121063049-9624-VRt7CYWKD936Sa29ycPsjA__server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 21 Nov 2007 11:18:51 +0100 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty=-=uni-oldenburg.de] > IRC calculations are black magic I have performed a number of IRC with B3LYP calculations and they can be tricky. I almost always observed that the calculation would go in one direction only and also fail after a few iterations. The solution to the calculation failing is to reduce the step-size. Here is a typical segment of my route: # b3lyp 6-31g* IRC(CALCFC,StepSize=5,MaxPoints=200,MaxCyc=40) The large number of MaxPoints here was to get a good approach to the end-points. This number is not so bad as it seems as the small step-size means that each step converges in 1-3 cycles and the IRC runs successfully. The second issue is getting the calculation to run in forward and reverse directions. Sometimes this works with B3LYP though it generally went in the same direction with either "reverse" or "forward". The solution I used for this was to start the two directions in two parallel calculations. If both were going in the same direction I would stop one and manually adjust the TS in the opposite direction and start from there (hence the "calcfc" in the above route!). Only a small adjustment based on the imaginary frequency was usually necessary to get the second direction. The results of one of my IRC calculations can be seen as an animation at "http://www.uq.edu.au/~uqjfinne/computational_chemistry/isomer.html" Cheers Justin -- Dr Justin Finnerty Rm W3-1-218 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Wed Nov 21 10:54:01 2007 From: "Justin Finnerty justin.finnerty!^!uni-oldenburg.de" To: CCL Subject: CCL:G: Quadcore v. Dualcore Message-Id: <-35676-071121062922-7865-nHCzSi2HiWVWoDdFG5ufgA+*+server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 21 Nov 2007 11:44:25 +0100 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty() uni-oldenburg.de] Hello, Performance needs to be tested on each code. Our observations for Gaussian03 are (Our nodes have dual-core AMDs and 2Gb RAM/cpu): A 4 node (linda) x 4 cpu (shared) job with exclusive node access performs about the same as a single node 4 (linda) x 4 cpu (shared) on a single 16cpu node. However the 16 cpu (shared) is significantly slower (almost twice as long). All jobs had the same total RAM available. Our node interconnect is gigabit ethernet and our trials on Infiniband interconnect show no advantage. Note these observations are for Gaussian03 and other codes could perform very differently. Our conclusion was that the total number of CPUs in the cluster was more important than the number of cpus/node. So our 4 cpu nodes give us more performance/euro than 16 cpu nodes as we can buy more than four 4 cpu nodes for one 16 cpu node. (Note the cost doesn't currently factor in running costs.) Cheers, Justin -- Dr Justin Finnerty Rm W3-1-218 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Wed Nov 21 11:33:00 2007 From: "akef afaneh akef_afnh||yahoo.com" To: CCL Subject: CCL:G: IRC calculation Message-Id: <-35677-071121090338-22634-GrLzU+N0/v4gWg7BmapThQ]~[server.ccl.net> X-Original-From: akef afaneh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1049373058-1195653801=:34098" Date: Wed, 21 Nov 2007 06:03:21 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: akef afaneh [akef_afnh-,-yahoo.com] --0-1049373058-1195653801=:34098 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I think that the forward pathway in your reaction is the reversed one. Why do not you try the reversed pathway? "Alexander Hoepker achoepker-.-gmail.com" wrote: Sent to CCL by: "Alexander Hoepker" [achoepker.:.gmail.com] I'm performing a forward IRC calculation starting with a transition state that has been optimized in Gaussian 03 in B3LYP (6/31G(d)) level of theory. The transition state was verified by one imaginary frequency for this particular deprotonation. my keywords are: #T B3LYP/6-31G(d) IRC=(CalcFC,Forward,MaxPoints=40) After only a couple of points the IRC appears to search backwards instead of forwards. IRC calculations are black magic for me and to be honest it is not surprising to me that the program confused the backward with the forward reaction coordinate. Could someone give me a hint as what I might be doing wrong or how I could tip the calculation in the right direction. Thanks a lot in advance. Alexhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Never miss a thing. Make Yahoo your homepage. --0-1049373058-1195653801=:34098 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
I think that the forward pathway in your reaction is the reversed one. Why do not you try the reversed pathway?


"Alexander Hoepker achoepker-.-gmail.com" <owner-chemistry(0)ccl.net> wrote:

Sent to CCL by: "Alexander Hoepker" [achoepker.:.gmail.com]
I'm performing a forward IRC calculation starting with a transition
state that has been optimized in Gaussian 03 in B3LYP (6/31G(d)) level
of theory. The transition state was verified by one imaginary
frequency for this particular deprotonation.

my keywords are: #T B3LYP/6-31G(d) IRC=(CalcFC,Forward,MaxPoints=40)

After only a couple of points the IRC appears to search backwards
instead of forwards. IRC calculations are black magic for me and to be
honest it is not surprising to me that the program confused the
backward with the forward reaction coordinate. Could someone give me a
hint as what I might be doing wrong or how I could tip the calculation
in the right direction. Thanks a lot in advance.

Alex


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




Never miss a thing. Make Yahoo your homepage. --0-1049373058-1195653801=:34098-- From owner-chemistry@ccl.net Wed Nov 21 12:04:00 2007 From: "Ulrich Scharfenort scharfenort.[A].ltt.rwth-aachen.de" To: CCL Subject: CCL:G: Strange Error in Gaussian Message-Id: <-35678-071121052519-1863-3bMyOfKH7ok6n7Bjyh5K8g[A]server.ccl.net> X-Original-From: Ulrich Scharfenort Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-15 Date: Wed, 21 Nov 2007 11:25:08 +0100 MIME-version: 1.0 Sent to CCL by: Ulrich Scharfenort [scharfenort+*+ltt.rwth-aachen.de] Hello, i hope someone has an solution for this strange problem. When i copy the *.chk file and the *.com file with an program and try to start it directly with Gaussian i get the following error: Unrecognized layer " ". C 1.27522 -0.25922 0. Error termination via Lnk1e in /opt/GAUSSIAN/LINUX_amd64/g03.d02/l101.exe at Wed Nov 21 but if i open the *.com file with an text editor and just save it (without any changes). Gaussian starts without any problem. I would be grateful for an solution to this strange problem. sincerly Ulrich Scharfenort From owner-chemistry@ccl.net Wed Nov 21 12:39:01 2007 From: "Michael Lanci mpl[A]jhu.edu" To: CCL Subject: CCL:G: PCM for DMF Message-Id: <-35679-071120141719-2981-1K98mofs5hVseCs+4cbV3w]=[server.ccl.net> X-Original-From: "Michael Lanci" Content-Type: multipart/alternative; boundary="----=_NextPart_000_001B_01C82B77.8257E4C0" Date: Tue, 20 Nov 2007 13:15:57 -0500 MIME-Version: 1.0 Sent to CCL by: "Michael Lanci" [mpl(!)jhu.edu] This is a multi-part message in MIME format. ------=_NextPart_000_001B_01C82B77.8257E4C0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I need to run a PCM calculation with dimethylformamide(DMF) as the solvent. From what I can find in the Gaussian user manuals the internal parameters are not defined for DMF and changing the dielectric constant will not sufficiently describe the system. Does anyone know how I could go about addressing this issue, or are there parameters that are available elsewhere? -Mike Michael Lanci Department of Chemistry Johns Hopkins University Baltimore, MD 21218 Phone: 410.516.7145 Fax: 410.516.8420 E-mail: mpl*jhu.edu ------=_NextPart_000_001B_01C82B77.8257E4C0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I need to run a PCM calculation with dimethylformamide(DMF) as the solvent.  From what = I can find in the Gaussian user manuals the internal parameters are not defined for = DMF and changing the dielectric constant will not sufficiently describe the system.  Does anyone know = how I could go about addressing this issue, or are there parameters that are available elsewhere?  

 

-Mike

=

 

 

Michael = Lanci

Department of = Chemistry

Johns Hopkins = University<= span style=3D'mso-no-proof:yes'>

Baltimore, MD 21218

 

Phone: = 410.516.7145

Fax: 410.516.8420

E-mail: = mpl*jhu.edu

 

------=_NextPart_000_001B_01C82B77.8257E4C0-- From owner-chemistry@ccl.net Wed Nov 21 13:16:01 2007 From: "Dr David S Coombes d.coombes^^ucl.ac.uk" To: CCL Subject: CCL: crystal structure codes Message-Id: <-35680-071121111654-4559-fgmcqWsJBX3C35vqwQRwUA*_*server.ccl.net> X-Original-From: "Dr David S Coombes" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Wed, 21 Nov 2007 15:40:34 -0000 MIME-Version: 1.0 Sent to CCL by: "Dr David S Coombes" [d.coombes^^^ucl.ac.uk] Gdis is very good! (gdis.sourceforge.net) -----Original Message----- > From: owner-chemistry!^!ccl.net [mailto:owner-chemistry!^!ccl.net] Sent: 21 November 2007 07:53 To: Coombes, David S Subject: CCL: crystal structure codes Sent to CCL by: "Alain Alloche" [alain.allouche(-)univ-provence.fr] Dear CCLers, Do you know crystal cell manipulation codes other than Cerius2 ? doing crystal surface cleaving and surface cell building ?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 Nov 21 13:49:01 2007 From: "Pedro Salvador pedro.salvador!^!udg.edu" To: CCL Subject: CCL: [NWCHEM, CCL] again about BSSE: in system of 145 molecules Message-Id: <-35681-071121114714-25638-MTxAZt+X4LwM6c4pQFPJpA:_:server.ccl.net> X-Original-From: Pedro Salvador Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 21 Nov 2007 17:15:58 +0100 MIME-Version: 1.0 Sent to CCL by: Pedro Salvador [pedro.salvador!=!udg.edu] Hi, you are probably only interested in seen how the basis functions of the water molecules affect the description of the cytosine-guanine pair and not about the BSSE in the description of each solvent molecule. Then you can take all solvent molecules as a single fragment and proceed. On the other hand, I imagine that the ghost orbital calculations must be very expensive, so I'd try first to use the closests water molecules' orbitals in the ghost orbital calculation and progresively add more and more water until the energy converges. Most probably, basis functions about 4-5 angstroms away from guanine-citosine atoms won't be necessary. Pedro Arvydas Tamulis tamulis..mserv.itpa.lt wrote: > Dear Colleagues, > > My friends support to run my DFT tasks calculating Guanine::Cytosine > conformations in the surrounding of real 143 solvent molecules, i.e. I > have 145 molecules in total in the supramolecular system. > How to evaluate the BSSE in this case? > > Cheers, > Arvydas > > On Wed, 21 Nov 2007, Maria Angels Carvajal wrote: > >> Dear all, >> I'm trying to compute the BSSE for a molecule. For the whole complex, I >> don�t have any problem, but when I change some of the atoms for Bqs, the >> calculation didn�t finish fine. >> I calculated BSSE for other molecules and using other basis sets and >> I had >> not any problem. I have this problem only in this case. >> Does someone know how can I overcome this? Thanks, >> From owner-chemistry@ccl.net Wed Nov 21 14:27:00 2007 From: "Igor Filippov Contr igorf[-]helix.nih.gov" To: CCL Subject: CCL:G: Strange Error in Gaussian Message-Id: <-35682-071121124143-1554-pjMDWPIrMuyinszzRoNrSg : server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 21 Nov 2007 12:41:08 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf---helix.nih.gov] It sounds like you might have run into a line break problem - it's different on unix and windows systems (\n on the former and \r\n on the latter). Opening the file and then saving it has probably resulted in the correction of the line breaks. Igor On Wed, 2007-11-21 at 11:25 +0100, Ulrich Scharfenort scharfenort.+/-.ltt.rwth-aachen.de wrote: > Sent to CCL by: Ulrich Scharfenort [scharfenort+*+ltt.rwth-aachen.de] > > Hello, > > i hope someone has an solution for this strange problem. > > When i copy the *.chk file and the *.com file with an program and try to > start it directly with Gaussian i get the following error: > > Unrecognized layer " > ". > C 1.27522 -0.25922 0. > Error termination via Lnk1e in > /opt/GAUSSIAN/LINUX_amd64/g03.d02/l101.exe at Wed Nov 21 > > but if i open the *.com file with an text editor and just save it > (without any changes). Gaussian starts without any problem. > > I would be grateful for an solution to this strange problem. > > sincerly > > Ulrich Scharfenort> > From owner-chemistry@ccl.net Wed Nov 21 14:59:00 2007 From: "Lukasz Cwiklik cwiklik()gmail.com" To: CCL Subject: CCL:G: Strange Error in Gaussian Message-Id: <-35683-071121132204-1261-Gbv8AaAYXW+jrp71wHM5NQ,server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 21 Nov 2007 20:21:49 +0200 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik!^!gmail.com] On Nov 21, 2007 12:25 PM, Ulrich Scharfenort scharfenort.(~).ltt.rwth-aachen.de wrote: > > Sent to CCL by: Ulrich Scharfenort [scharfenort+*+ltt.rwth-aachen.de] > > Hello, > > i hope someone has an solution for this strange problem. > > When i copy the *.chk file and the *.com file with an program and try to > start it directly with Gaussian i get the following error: > > Unrecognized layer " > ". > C 1.27522 -0.25922 0. > Error termination via Lnk1e in > /opt/GAUSSIAN/LINUX_amd64/g03.d02/l101.exe at Wed Nov 21 > > but if i open the *.com file with an text editor and just save it > (without any changes). Gaussian starts without any problem. > > I would be grateful for an solution to this strange problem. Hi, Sounds like typical problem with text file encoding. Are you copying your files only between 2 Linux machines? Or maybe you have Windows involved somehow? Also, what program you are using for copying and what text editor? Looking at the G03 source code I noticed that ""." is added just as a comment, it is not read from your input. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Wed Nov 21 15:33:00 2007 From: "Close, David M. CLOSED+/-mail.etsu.edu" To: CCL Subject: CCL:G: Strange Error in Gaussian Message-Id: <-35684-071121132644-4965-EbehKq4ZMINKcP/qQbFjeA a server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 21 Nov 2007 13:26:27 -0500 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED:_:mail.etsu.edu] Ulrich: You don't say how you prepared the original file. However the failure is in Link1, so Gaussian is having trouble reading the input file. Sometimes this results from using a DOS editor to input information to a UNIX environment. UNIX tends to have troubles with old DOS characters such a carriage returns. These characters are hidden, so you editor doesn't show them. If this is your problem, you can find useful DOS to Unix conversion programs that come with the usual FORTRAN editors on the www. Regards, Dave Close. -----Original Message----- > From: owner-chemistry-$-ccl.net [mailto:owner-chemistry-$-ccl.net]=20 Sent: Wednesday, November 21, 2007 5:25 AM To: Close, David M. Subject: CCL:G: Strange Error in Gaussian Sent to CCL by: Ulrich Scharfenort [scharfenort+*+ltt.rwth-aachen.de] Hello, i hope someone has an solution for this strange problem. When i copy the *.chk file and the *.com file with an program and try to start it directly with Gaussian i get the following error: Unrecognized layer " ". C 1.27522 -0.25922 0. Error termination via Lnk1e in /opt/GAUSSIAN/LINUX_amd64/g03.d02/l101.exe at Wed Nov 21 but if i open the *.com file with an text editor and just save it (without any changes). Gaussian starts without any problem. I would be grateful for an solution to this strange problem. sincerly Ulrich Scharfenort -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Nov 21 16:09:00 2007 From: "Daniel Glossman-Mitnik dglossman||gmail.com" To: CCL Subject: CCL: solar cells efficiency parameters Message-Id: <-35685-071121135941-31831-3OIKaVGVXUgZw/fRa4qjUw#server.ccl.net> X-Original-From: "Daniel Glossman-Mitnik" Date: Wed, 21 Nov 2007 13:59:37 -0500 Sent to CCL by: "Daniel Glossman-Mitnik" [dglossman:-:gmail.com] Dear netters: When studying solar cells, specially DSSCs, one needs to estimate the efficiency of the materials used for the construction of that solar cell. The way that this is usually performed is by constructing the I-V curve under standard illumination for a given molecule or material. From this curve it is possible to get some parameters like the short-circuit photocurrent Isc, the open-circuit voltage Voc, of course I and V, the fill factor FF, etc. With all this parameters one is able to estimate the efficiency of the solar cell. From the theoretical point of view, there are programs that can simulate computationally the I-V curve, and from there, to extract the needed parameters. My question is: Is it possible to calculate the needed parameters to emitate the efficiency based solely in terms of quantum chemistry calculations? I am thinking that something can be done in terms of orbitals or the ionization potential and electron affinity. I will be grateful if you can send me informations about literature (journal, books, web pages) where this problem has been considered. Best regards, Daniel Glossman-Mitnik From owner-chemistry@ccl.net Wed Nov 21 16:44:00 2007 From: "Alex Allardyce aa|chemaxon.com" To: CCL Subject: CCL: Looking for a structure to name conversion software Message-Id: <-35686-071121140341-2410-DZuXyjDIq5ZRCSkF9O66hA:-:server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------090808060304070503070607" Date: Wed, 21 Nov 2007 14:03:26 -0500 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa++chemaxon.com] This is a multi-part message in MIME format. --------------090808060304070503070607 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit HI, Yes ChemAxon can help there. Either you can run these structures through our structure to name Calculator Plugin (http://www.chemaxon.com/product/st2name.html) as batch from the command line utility cxcalc (http://www.chemaxon.com/marvin/doc/user/calc.html) or if you want an application GUI then the same Plugin is implemented in Instant JChem (http://www.chemaxon.com/product/ijc.html). If you are an academic user all of our software is free, more information and sign up: http://www.chemaxon.com/acpack_conditions.html Cheers Alex Alex Allardyce Dir. Marketing, ChemAxon drmsaravanan=aim.com wrote: > > Hi All, > > Is there any tool to convert 1000 structures to name at a stretch? it > would be better if it is available freely. > > regards, > > M. Saravanan > ------------------------------------------------------------------------ > *Check Out the new free AIM(R) Mail* > > -- Unlimited storage and industry-leading spam and email virus protection. -- --------------090808060304070503070607 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit HI,

Yes ChemAxon can help there.

Either you can run these structures through our structure to name Calculator Plugin (http://www.chemaxon.com/product/st2name.html) as batch from the command line utility cxcalc (http://www.chemaxon.com/marvin/doc/user/calc.html) or if you want an application GUI then the same Plugin is implemented in Instant JChem (http://www.chemaxon.com/product/ijc.html).

If you are an academic user all of our software is free, more information and sign up: http://www.chemaxon.com/acpack_conditions.html

Cheers
Alex
Alex Allardyce
Dir. Marketing, ChemAxon
drmsaravanan=aim.com wrote:

Hi All,

Is there any tool  to convert 1000 structures to name at a stretch? it would be better if it is available freely.

regards,

M. Saravanan
Check Out the new free AIM(R) Mail -- Unlimited storage and industry-leading spam and email virus protection.

--
--------------090808060304070503070607-- From owner-chemistry@ccl.net Wed Nov 21 17:22:00 2007 From: "Jerome Kieffer jerome.Kieffer ~ terre-adelie.org" To: CCL Subject: CCL:G: Strange Error in Gaussian Message-Id: <-35687-071121143203-21673-Xw92UGia7mZ4AtJGa7vVuA|,|server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Wed, 21 Nov 2007 20:33:58 +0100 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer+*+terre-adelie.org] On Wed, 21 Nov 2007 11:25:08 +0100 "Ulrich Scharfenort scharfenort.]_[.ltt.rwth-aachen.de" wrote: > i hope someone has an solution for this strange problem. >=20 > When i copy the *.chk file and the *.com file with an program and try to > start it directly with Gaussian i get the following error: >=20 > Unrecognized layer " > ". > C 1.27522 -0.25922 0. > Error termination via Lnk1e in > /opt/GAUSSIAN/LINUX_amd64/g03.d02/l101.exe at Wed Nov 21 >=20 > but if i open the *.com file with an text editor and just save it > (without any changes). Gaussian starts without any problem. This typically looks like a dos-unix conversion problem. try to do a dos2unix on your file before submitting it G03. Regards. --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org From owner-chemistry@ccl.net Wed Nov 21 17:53:00 2007 From: "Sabry Ahmed sabry.ea^-^gmail.com" To: CCL Subject: CCL:G: How to Identify and correct for Hindered Rotors in G03 Message-Id: <-35688-071121131127-25598-2hwD1ga3qFVWd/FbNh5DVQ:-:server.ccl.net> X-Original-From: "Sabry Ahmed" Content-Type: multipart/alternative; boundary="----=_Part_29423_27210606.1195664735735" Date: Wed, 21 Nov 2007 20:05:35 +0300 MIME-Version: 1.0 Sent to CCL by: "Sabry Ahmed" [sabry.ea . gmail.com] ------=_Part_29423_27210606.1195664735735 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello CCLers, I'm trying to correct for hindered rotation modes using the keyword Freq=HinderedRotor in G03. In fact I have no idea how to do that; I mean the identification and the correction. For the reactant the job terminated successfully but I don't know what I should get from the output. Fot the TS, the job failed with the following error message: --------------------------------------------------------------------------------- Check correspondance between vibrational and internal rotation modes frequencies in cm**-1 1 2 3 Frequencies --- 95.0468 155.4019 177.3364 -1474.4902 0.0101 0.0562 -0.0333 92.0838 -0.9973 0.4231 0.6332 136.3765 -0.2606 0.8307 0.3015 155.3244 0.4631 -0.8491 -0.9191 195.3921 -0.6826 0.4576 0.8660 343.8586 -0.8442 0.7230 0.8824 ---------------------------------------------------------------------------- One-to-one correspondance not acheived Constrained mode 2 likely source of the problem Bond # Atoms 1 1 2 0.00000 2 2 3 0.07105 3 3 8 0.12548 4 8 9 0.74224 Freeze coordinate 27 Freeze coordinate 28 Freeze coordinate 29 Freeze coordinate 30 Redo normal mode analysis with added constraints Number of internal rotation degrees of freedom = 3 NNew= 7 NTest= 3 NB= 4 IFrz= 1 IBar= 1 ICyc= 0 Problem with the number of degrees of freedom Error termination via Lnk1e in C:\G03W\l716.exe at Sat Nov 10 22:37:32 2007. -------------------------------------------------------------------------------------------------------------------------------- I don't understand what the message means. I shall be very grateful if anyone can help me (using a simple example would be fine) Thank you in advance. Sabry Ahmed -- Sabry El-Taher Ahmed Cairo University Faculty of Science Department of Chemistry Cairo, Egypt. ------=_Part_29423_27210606.1195664735735 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hello CCLers,

I'm trying to correct for hindered rotation modes using the keyword  Freq=HinderedRotor in G03.
In fact I have no idea how to do that; I mean the identification and the correction.  For the reactant the job terminated successfully
but I don't know what I should get from the output.  Fot the TS, the job failed with the following error message:
---------------------------------------------------------------------------------
 Check correspondance between vibrational and internal rotation modes
 frequencies in cm**-1
                           1         2         3
     Frequencies ---    95.0468  155.4019  177.3364
      -1474.4902         0.0101    0.0562   -0.0333
         92.0838        -0.9973    0.4231    0.6332
        136.3765        -0.2606    0.8307    0.3015
        155.3244         0.4631   -0.8491   -0.9191
        195.3921        -0.6826    0.4576    0.8660
        343.8586        - 0.8442    0.7230    0.8824
 ----------------------------------------------------------------------------
 One-to-one correspondance not acheived
 Constrained mode   2 likely source of the problem
 Bond #  Atoms
  1     1   2    0.00000
  2     2   3    0.07105
  3     3   8    0.12548
  4     8   9    0.74224
 Freeze coordinate  27
 Freeze coordinate  28
 Freeze coordinate  29
 Freeze coordinate  30
 Redo normal mode analysis with added constraints
 Number of internal rotation degrees of freedom =   3
 NNew=    7 NTest=    3 NB=    4 IFrz=    1 IBar=    1 ICyc=    0
 Problem with the number of degrees of freedom
 Error termination via Lnk1e in C:\G03W\l716.exe at Sat Nov 10 22:37:32
2007.
 --------------------------------------------------------------------------------------------------------------------------------
 
I don't understand what the message means.  I shall be very grateful if anyone can help me (using a simple example would be fine)
Thank you in advance.

Sabry Ahmed


--
Sabry El-Taher Ahmed
Cairo University
Faculty of Science
Department of Chemistry
Cairo, Egypt.
------=_Part_29423_27210606.1195664735735--