[QE-users] occupation in biological molecules and band gap
José Xavier
jxln_karate at yahoo.com.br
Thu Nov 4 08:25:30 CET 2021
Dear,
Sorry.
The group I'm working with has published some papers describing the properties of the crystal of biomolecules using castep code and I would like to introduce the QE to perform similar calculations. Then, I am now trying to reproduce a paper published by the group last year to set up the input files for the next calculation that I will perform, also with the crystal structure of a biomolecule.
I do not know if I can attach the paper here, so this is the reference: R. L. Araújo et al., Chemical Physics Letters 761 (2020) 138033.
The band gap for Dopamine was 3.8 eV, and the other papers published by them showed values between 3-5 eV. That is why I have asked about the better option for the occupancy of semiconductors. It is one of the points that I'm trying to understand in QE to add to the calculations.
It is the input file
&control
calculation = 'scf',
nstep = 1500,
etot_conv_thr = 5.0D-7,
forc_conv_thr = 1.0D-4,
verbosity = 'high',
/
&system
ibrav = 8,
a = 10.50228,
b = 10.89998,
c = 7.70059,
nat = 96,
ntyp = 5,
ecutwfc = 73.49,
ecutrho = 293.99,
input_dft = 'PBE',
vdw_corr = 'ts',
/
&electrons
electron_maxstep = 500,
conv_thr = 1.0D-8,
/
&ions
/
&cell
/
ATOMIC_SPECIES
Cl 35.452702 Cl.upf
C 12.011000 C.upf
N 14.006700 N.upf
O 15.999400 O.upf
H 1.007900 H.upf
ATOMIC_POSITIONS (angstrom)
Cl 0.0817992817 3.5576016812 2.0615460194
C 5.5672207516 2.3820020182 1.5383881642
C 6.8676172680 2.3016151531 2.0378186594
C 7.6740917486 1.2139979213 1.7109111992
C 7.1708614134 0.2052409474 0.8660364342
C 5.8641017691 0.2888392074 0.3824664792
C 5.0461091419 1.3745015880 0.7211106768
C 3.6078113637 1.4316201905 0.2725853451
C 2.7518815143 0.4607516679 1.0837652041
N 1.2927740324 0.7293581046 0.9097604338
O 8.9420606908 1.0405633732 2.1969666347
O 7.9421528767 -0.8592157994 0.4969485133
H 4.9507875742 3.2382085016 1.7978112316
H 7.2567722381 3.0757711119 2.6983831238
H 5.4944176415 -0.5103602212 -0.2609621157
H 3.5211750076 1.1867086798 -0.7944499632
H 3.2341044736 2.4553300348 0.4002708665
H 2.9544617954 0.5610191735 2.1528589679
H 2.9305129146 -0.5797510968 0.7909394044
H 1.0163150923 0.8290194264 -0.0876428360
H 0.7377473441 -0.0519386975 1.3201503246
H 1.0094717266 1.6180109698 1.3674476912
H 9.3583518315 1.9253421323 2.3588599841
H 8.7739063725 -0.9001600265 1.0247860732
Cl 10.4204815314 9.0075931626 2.0615460194
C 4.9350600615 7.8319934996 1.5383881642
C 3.6346635451 7.7516066345 2.0378186594
C 2.8281890645 6.6639894027 1.7109111992
C 3.3314193997 5.6552324288 0.8660364342
C 4.6381790440 5.7388306888 0.3824664792
C 5.4561716712 6.8244930694 0.7211106768
C 6.8944694494 6.8816116719 0.2725853451
C 7.7503992987 5.9107431493 1.0837652041
N 9.2095067806 6.1793495860 0.9097604338
O 1.5602201223 6.4905548545 2.1969666347
O 2.5601279363 4.5907756820 0.4969485133
H 5.5514932389 8.6881999830 1.7978112316
H 3.2455085750 8.5257625933 2.6983831238
H 5.0078631716 4.9396312602 -0.2609621157
H 6.9811058055 6.6367001612 -0.7944499632
H 7.2681763394 7.9053215162 0.4002708665
H 7.5478190177 6.0110106549 2.1528589679
H 7.5717678985 4.8702403846 0.7909394044
H 9.4859657207 6.2790109078 -0.0876428360
H 9.7645334690 5.3980527839 1.3201503246
H 9.4928090865 7.0680024512 1.3674476912
H 1.1439289816 7.3753336137 2.3588599841
H 1.7283744406 4.5498314548 1.0247860732
Cl 0.0817992817 1.8923898002 5.9118373550
C 5.5672207516 3.0679894631 5.3886794997
C 6.8676172680 3.1483763283 5.8881099949
C 7.6740917486 4.2359935601 5.5612025347
C 7.1708614134 5.2447505339 4.7163277697
C 5.8641017691 5.1611522740 4.2327578147
C 5.0461091419 4.0754898934 4.5714020123
C 3.6078113637 4.0183712909 4.1228766806
C 2.7518815143 4.9892398135 4.9340565396
N 1.2927740324 4.7206333768 4.7600517694
O 8.9420606908 4.4094281082 6.0472579702
O 7.9421528767 6.3092072808 4.3472398488
H 4.9507875742 2.2117829797 5.6481025671
H 7.2567722381 2.3742203695 6.5486744594
H 5.4944176415 5.9603517026 3.5893292198
H 3.5211750076 4.2632828016 3.0558413723
H 3.2341044736 2.9946614466 4.2505622020
H 2.9544617954 4.8889723078 6.0031503034
H 2.9305129146 6.0297425782 4.6412307399
H 1.0163150923 4.6209720549 3.7626484995
H 0.7377473441 5.5019301789 5.1704416601
H 1.0094717266 3.8319805115 5.2177390267
H 9.3583518315 3.5246493491 6.2091513196
H 8.7739063725 6.3501515079 4.8750774087
Cl 10.4204815314 7.3423812815 5.9118373550
C 4.9350600615 8.5179809445 5.3886794997
C 3.6346635451 8.5983678096 5.8881099949
C 2.8281890645 9.6859850415 5.5612025347
C 3.3314193997 10.6947420153 4.7163277697
C 4.6381790440 10.6111437554 4.2327578147
C 5.4561716712 9.5254813747 4.5714020123
C 6.8944694494 9.4683627722 4.1228766806
C 7.7503992987 10.4392312948 4.9340565396
N 9.2095067806 10.1706248581 4.7600517694
O 1.5602201222 9.8594195896 6.0472579702
O 2.5601279363 11.7591987621 4.3472398488
H 5.5514932389 7.6617744611 5.6481025671
H 3.2455085750 7.8242118508 6.5486744594
H 5.0078631716 11.4103431839 3.5893292198
H 6.9811058055 9.7132742830 3.0558413723
H 7.2681763394 8.4446529280 4.2505622020
H 7.5478190177 10.3389637892 6.0031503034
H 7.5717678985 11.4797340595 4.6412307399
H 9.4859657207 10.0709635363 3.7626484995
H 9.7645334690 10.9519216602 5.1704416601
H 9.4928090865 9.2819719929 5.2177390267
H 1.1439289816 8.9746408304 6.2091513196
H 1.7283744406 11.8001429893 4.8750774087
K_POINTS (automatic)
2 2 2 0 0 0
Em quinta-feira, 4 de novembro de 2021 03:06:30 BRT, Kazume NISHIDATE <nisidate at iwate-u.ac.jp> escreveu:
> would like to ask if you could tell me why this question generates so different answers.
It is partly because you did not provide the detailed information on your calculation.
I supposed it is a crystal composed of molecules and you applied some
k-point mesh to incorporate its periodicity. I thought that the system
might be in a semiconducting state since you were interested in the
gap value. In that case, you should apply the 'smearing' method.
If you are calculating an isolated molecule in vacuume with only the
gamma for the k-point, then the 'fixed' method is a good choice since
the occupancy can be defined explicitly at the gamma.
- note
The 'nbnd' is the number of band. You should include sufficient empty
bands to draw a nice band/dos structure.
best regards
kazume NISHIDATE
敬具 西館数芽
nisidate at iwate-u.ac.jp
kazume.nishidate at gmail.com
2021年11月4日(木) 14:09 José Xavier <jxln_karate at yahoo.com.br>:
> Dear,
>
> Thank you for your explanation.
> I'll try both occupancies to see if the results of bandgap and DOS are very different. When I got the values, I can post the differences here.
>
> I would like to ask if you could tell me why this question generates so different answers. As just like in the tutorials I saw, each one gave me a different answer.
>
> Best wishes,
> José Xavier
>
>
> Em terça-feira, 2 de novembro de 2021 00:41:19 BRT, Mahmoud Payami Shabestari <mpayami at aeoi.org.ir> escreveu:
>
>
>
>
>
>
> Dear Xavier,
>
>
>
>> So, I can use the Fixed occupation and, if the energy levels show a small bandgap, I introduce the >Smearing. Is it right?
>
>
>
> Yes, exactly.
>
>
>
>
>>If yes, I just have to add the nbnd function in the input file?
>
>
>
> Yes. It suffices to put nbnd equal to N/2 + 1 (N is number of electrons).
>
>
>
> Mahmoud
>
>> From: xavier neto via users <users at lists.quantum-espresso.org>
>>
>> To: Mahmoud Payami Shabestari <mpayami at aeoi.org.ir>, Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
>> Date: Mon, 1 Nov 2021 21:04:31 -0300
>> Subject: [QE-users] occupation in biological molecules and band gap
>>
>> Dear Mahmoud Payami,
>>
>> Thank you for your answer. It helps me a lot.
>>
>> So, I can use the Fixed occupation and, if the energy levels show a small bandgap, I introduce the Smearing. Is it right?
>>
>>
>>
>> About the second question. I've read that the result of HOMO - LUMO, obtained after the SCF calculation, can give the bandgap. Can I obtain the bandgap in that way? If yes, I just have to add the nbnd function in the input file?
>>
>> On 11/1/21 02:04, Mahmoud Payami Shabestari wrote:
>>
>>>
>>> Dear José Xavier,
>>>
>>> Hi.
>>>
>>> Smearing for the occupations is used when the levels near HOMO are so close (commonly in metals near Fermi level) that in consecutive iterations they may exchange positions and lead to nonconvergence. For semiconductors with 3-5 eV gap I think it won't help.
>>>
>>> Bests
>>>
>>>
>>> Mahmoud Payami
>>>
>>> NSTRI, AEOI, Tehran, Iran
>>>
>>>
>>>
>>>
>>>
>>>> From: José Xavier via users <users at lists.quantum-espresso.org>
>>>> To: "users at lists.quantum-espresso.org" <users at lists.quantum-espresso.org>
>>>> Date: Mon, 1 Nov 2021 00:18:55 +0000 (UTC)
>>>> Subject: [QE-users] occupation in biological molecules and band gap
>>>>
>>>> Dear all,
>>>>
>>>> I'm new in QE. The group that I'm working with usually calculates the properties of biologically relevant molecules, like amino acids, hormones, neurotransmitters, and drugs, and I would like to introduce the QE code to the group. Their previous papers have shown that the bandgap of these crystals is something between 3-5 eV, which I understand to be in the semiconductor range.
>>>>
>>>> I've watched/read some tutorials about QE, and some of these showed that the occupation of semiconductors should be "smearing", other ones that it should be "fixed", but no one showed calculations with this kind of molecules. What value should I use for the SCF and electronic calculations of the crystals that I'm going to work on (amino acids, hormones, neurotransmitters, and drugs)?
>>>>
>>>> *Are there any differences when the molecule has a metal, like the Heme group?
>>>>
>>>> Besides, I would like to ask if there is a calculation that I could perform to obtain the bandgap of these molecules. Is it only possible if I create the band structure figure and calculate the difference between the peaks in VB and CB?
>>>>
>>>> Thank you for your help,
>>>>
>>>> Sincerely,
>>>> José Xavier
>>>>
>>>> _______________________________________________
>>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>>>> users mailing list users at lists.quantum-espresso.org
>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>>
>>>
>>>
>>
>
>
>
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