[DFTB-Plus-User] R: R: R: UV-Vis Calculations and in error (NrOfExcitations)

Thu Feb 16 16:14:58 CET 2023

Dear Thomas,

“Can you please send the geometry and input file for this job?”

Yes attached

Sure, but why do you set 'Charge = -3' if the total charge is +3? 

Sorry, in the previous mail I ported the wrong charges. The correct one are

Protein -2; 

ligand -1;

tot -3 

As just set in the input file (attached protein_ligand).

“I can not reproduce this. For me the  recipes_DFTB+/linresp/macromolecule job runs smooth with dftb+ 22.2 (I don't expect dftb+21.2 to be any different).”

I am also attaching (tutorial) files related to the error that I get when I ran the tutorial. Maybe some error during the installation of  the software?

Thanks for your help

Best,

Daniele.

Da: DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> Per conto di Thomas Niehaus
Inviato: giovedì 16 febbraio 2023 11:12
A: dftb-plus-user at mailman.zfn.uni-bremen.de
Oggetto: Re: [DFTB-Plus-User] R: R: UV-Vis Calculations and in error (NrOfExcitations)

Dear Daniele,

On 2/16/23 9:58 AM, daniele.veclani at isof.cnr.it <mailto:daniele.veclani at isof.cnr.it>  wrote:

Dear Thomas,

“when you say the system was well optimized, did you check the state occupations at the final structure (-> band.out)?”

Yes, I check the state occupations at the final structure (band.out) and no fractional occupations was observed.

I report below a fragment of the band.out file corresponding to the HOMO-LUMO gap:

“  1884    -4.784  2.00000

  1885    -4.677  2.00000

  1886    -4.581  2.00000

  1887    -4.314  2.00000

  1888    -2.723  0.00000

  1889    -2.124  0.00000

  1890    -1.949  0.00000”

Can you please send the geometry and input file for this job?

Is your system zwitterionic, are the ligands maybe charged....

Yes, protein have a charge of +4 while ligand have a -1 charge (total charge +3). I have to respect these charges because I have to study the system at a given pH.

Sure, but why do you set 'Charge = -3' if the total charge is +3?  

Did you run the tutorial with the geometry and input file for that tutorial?

Yes, I ran the geometry and input file found in recipes_DFTB+/linresp/macromolecule, however I obtain then same error.

I use a 21.2 version of DFTB+ software.

I can not reproduce this. For me the  recipes_DFTB+/linresp/macromolecule job runs smooth with dftb+ 22.2 (I don't expect dftb+21.2 to be any different).

Best Thomas

Best,

Daniele.

Da: DFTB-Plus-User  <mailto:dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> Per conto di Thomas Niehaus
Inviato: mercoledì 15 febbraio 2023 17:27
A: dftb-plus-user at mailman.zfn.uni-bremen.de <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de> 
Oggetto: Re: [DFTB-Plus-User] R: UV-Vis Calculations and in error (NrOfExcitations)

Dear Daniele,

when you say the system was well optimized, did you check the state occupations at the final structure (-> band.out)? Is your system zwitterionic, are the ligands maybe charged....

Did you run the tutorial with the geometry and input file for that tutorial? I don't understand what you mean with relative geometry.

Best Thomas

On 2/15/23 5:03 PM, daniele.veclani at isof.cnr.it <mailto:daniele.veclani at isof.cnr.it>  wrote:

Dear Thomas,

first of all thanks for your reply, no my system is a protein fragment + ligand, and this system was well optimized before the UV-vis calculation. I don't understand where the metallic character can come from. However I get the same error even if I run the tutorial input (with relative geometry) found in the DTFB+ recipes (recipes_DFTB+/linresp/macromolecule).

And I don't understand why also the tutorial calculation crashes.

Do you have any suggestion?

Best regards,

Daniele.

Da: DFTB-Plus-User  <mailto:dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> Per conto di Thomas Niehaus
Inviato: mercoledì 15 febbraio 2023 16:56
A: dftb-plus-user at mailman.zfn.uni-bremen.de <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de> 
Oggetto: Re: [DFTB-Plus-User] UV-Vis Calculations and in error (NrOfExcitations)

Dear Daniele,

it seems that your system is metallic. There are several fractional occupations. This means that the response matrix to diagonalize becomes gigantic and that there are clusters of near zero excitation energies which the iterative eigensolver can not separate. 

I would suggest to identify the origin of the metallic behaviour. Is the structure chemically sound?

Best regards

Thomas  

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-- 
Prof. Dr. Thomas Niehaus
Institut Lumière Matière
UMR5306 CNRS
Université Claude Bernard Lyon 1
Domaine Scientifique de La Doua
10 rue Ada Byron 
69622 Villeurbanne CEDEX, France
--
Office: Brillouin building, 4th floor, room 006
Tel: +33 472 431 571
Home page: http://ilm-perso.univ-lyon1.fr/~tniehaus
Lab: http://ilm.univ-lyon1.fr

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-- 
Prof. Dr. Thomas Niehaus
Institut Lumière Matière
UMR5306 CNRS
Université Claude Bernard Lyon 1
Domaine Scientifique de La Doua
10 rue Ada Byron 
69622 Villeurbanne CEDEX, France
--
Office: Brillouin building, 4th floor, room 006
Tel: +33 472 431 571
Home page: http://ilm-perso.univ-lyon1.fr/~tniehaus
Lab: http://ilm.univ-lyon1.fr

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