From NWChem
Viewed 1822 times, With a total of 5 Posts
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Posts 63
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| 7:44:16 AM PST - Fri, Nov 28th 2014 |
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Hi.
I am a beginner in nwchem.
I was trying to calculate interaction between two monomers using open-shell DFT. The input script i was using:
title 'dft-energy'
start dimer
geometry units angstrom
symmetry c1
C 2.965 23.359 58.764
C 1.892 22.522 58.067
O 2.178 21.539 57.399
C 3.074 22.934 60.212
C 4.384 23.352 60.901
N 4.641 24.608 61.248
C 5.423 22.607 61.249
C 5.863 24.629 61.854
N 6.338 23.431 61.871
H 3.814 23.193 58.326
N 2.739 24.753 58.631
H 2.603 25.170 59.371
O 2.533 26.305 61.093
C 2.375 27.069 62.059
N 0.276 24.751 62.891
C 0.008 26.050 62.356
C -0.203 26.009 60.830
O -0.082 24.982 60.186
C 1.059 27.102 62.775
O 3.249 27.900 62.464
H 1.049 24.613 63.117
H -0.829 26.341 62.751
H 0.671 27.982 62.652
H 1.229 26.997 63.724
end
charge 0
basis "ao basis"
* library 6-31G
bq* library * 6-31G
end
dft
odft
xc pbe0
direct
iterations 700
end
bsse
mon first 1 2 3 4 5 6 7 8 9 10 11 12
mon second 13 14 15 16 17 18 19 20 21 22 23 24
end
task dft energy
Now the default the multiplicity assigned here is 1. So, I am getting this error:
Summary of "ao basis" -> "ao basis" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
C 6-31G 5 9 3s2p
O 6-31G 5 9 3s2p
N 6-31G 5 9 3s2p
H 6-31G 2 2 2s
Caching 1-el integrals
number of electrons : 67
multiplicity : 1
------------------------------------------------------------------------
no. of electrons and multiplicity not compatible 67
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
49: task dft energy
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error in the input file
------------------------------------------------------------------------
I am really getting nowhere to perform this calculation with it.
Do I have to define multiplicity for each monomer, as the no. of electrons are different ?
Is it possible that nwchem automatically assign multiplicity ?
Please help.
Thank you.
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Edited On 3:55:08 AM PST - Wed, Dec 3rd 2014 by Neo
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Clicked A Few Times
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Posts 8
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| 12:55:11 AM PST - Mon, Dec 1st 2014 |
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| Your structure looks very wrong for something realistic. Fix this and your problem will ikely go away. The nitrogens have 2 bonds, the carbons are somewhat carbene like. I think you need to addmore hydrogens to properly saturate the structures, if that is the intent.
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
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Posts 1267
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| 12:25:05 PM PST - Mon, Dec 1st 2014 |
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Neo
The molecule you defined in your input file has an odd number of electrons, therefore it cannot be a singlet (default value in NWChem). You can either define it as a doublet (mult 2), quartet (mult 4), etc ...
http://www.nwchem-sw.org/index.php/Release65:Density_Functional_Theory_for_Molecules#ODFT_...
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Gets Around
Threads 30
Posts 63
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| 5:05:14 AM PST - Tue, Dec 2nd 2014 |
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Quote:Brose Dec 1st 12:55 amYour structure looks very wrong for something realistic. Fix this and your problem will ikely go away. The nitrogens have 2 bonds, the carbons are somewhat carbene like. I think you need to addmore hydrogens to properly saturate the structures, if that is the intent.
Thank you for your suggestion regarding addition of more hydrogen.
So, my final script became like:
title 'r_Hb_e'
start dimer
geometry units angstrom
C 2.965 23.359 58.764
C 1.892 22.522 58.067
O 2.178 21.539 57.399
C 3.074 22.934 60.212
C 4.384 23.352 60.901
N 4.641 24.608 61.248
C 5.423 22.607 61.249
C 5.863 24.629 61.854
N 6.338 23.431 61.871
H 3.814 23.193 58.326
H 6.286 25.383 62.197
H 5.515 21.694 61.097
H 4.129 25.286 61.117
H 2.989 21.969 60.262
H 2.328 23.310 60.705
N 2.739 24.753 58.631
H 2.603 25.170 59.371
O 2.533 26.305 61.093
C 2.375 27.069 62.059
N 0.276 24.751 62.891
C 0.008 26.050 62.356
C -0.203 26.009 60.830
O -0.082 24.982 60.186
C 1.059 27.102 62.775
O 3.249 27.900 62.464
H 1.049 24.613 63.117
H -0.829 26.341 62.751
H 0.671 27.982 62.652
H 1.229 26.997 63.724
end
basis "ao basis"
* library 6-31G
bq* library * 6-31G
end
dft
odft
mult 4
xc pbe0
direct
iterations 1000
end
bsse
mon first 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
mon second 18 19 20 21 22 23 24 25 26 27 28 29 mult 4
end
task dft energy
But this code is giving a different error:
NWChem DFT Module
-----------------
'r_Hb_e'
bas_tag_lib: tag does not refer to an atom 0
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
0:
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error in the input file
------------------------------------------------------------------------
For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation
For further details see manual section:
41:41:bas_tag_lib: tag does not refer to an atom:: -1
(rank:41 hostname:login1.cmmacs.ernet.in pid:63259):ARMCI DASSERT fail. ../../ga-5-3/armci/src/common/armci.c:ARMCI_Error():208 cond:0
Last System Error Message from Task 41:: Illegal seek
What is bas_tag_lib problem according to the error report ?
Definitely the first time I'm having this particular issue.
Please help with my code.
thank you.
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Edited On 11:38:59 PM PST - Tue, Dec 2nd 2014 by Neo
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Clicked A Few Times
Threads 2
Posts 8
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| 5:17:28 AM PST - Tue, Dec 2nd 2014 |
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| The blank line in the geometry may need to be removed. The structure still looks strange, the carbonyls dangling might need to be bonded to something else. Perhaps hydrogen to make an 'aldehyde'? Again, just blindly guessing since I do not know the project.
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Gets Around
Threads 30
Posts 63
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| 5:51:47 AM PST - Tue, Dec 2nd 2014 |
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Quote:Brose Dec 2nd 5:17 amThe blank line in the geometry may need to be removed. The structure still looks strange, the carbonyls dangling might need to be bonded to something else. Perhaps hydrogen to make an 'aldehyde'? Again, just blindly guessing since I do not know the project.
Actually that first paragraph shows Histidine amino acid and the second shows the co-ordinates of Aspartate.
I have tried removing the space but it showed same 'bas_tag_lib: tag does not refer to an atom' error message.
I specifically needed the data for interaction of 17th and 18th atom, so tried the bsse approach with rest of molecule treating them as interacting monomer.
So, a little help with the code would be highly useful.
thank you..
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Edited On 12:08:19 AM PST - Wed, Dec 3rd 2014 by Neo
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