[ase-users] [gpaw-users] Embedded GW calculations with ASE and GPAW

[marc]

Dear Asmus,

I'm trying to run QM/MM calculations for a molecule called alpha-MAND 
(see attached structure). I would like to calculate the energy levels 
(HOMO and LUMO) of this molecule including the environment (which is 
composed of the same molecule). An example of such work can be find here 
<https://pubs.rsc.org/en/content/articlepdf/2018/mh/c8mh00921j>. 
Ultimately, I would like to perform similar work with ASE/GPAW, but I'm 
not sure it is possible.

 From what I understand, I would need a force field for the MM 
calculator, is it correct?

Best regards,
Marc

On 5/30/19 5:57 PM, Asmus Ougaard Dohn wrote:
> Dear Marc,
>
> Which force field(s) are we talking about, and for what molecules?
>
> Best,
>
> Asmus
>
> On 30 May 2019, at 07.44, marc <marc.barbry at mailoo.org 
> <mailto:marc.barbry at mailoo.org>> wrote:
>
>> Dear Asmus,
>>
>> Thanks a lot for your answer. It seems to be what I'm looking for, at 
>> least part of it. Unfortunately I have very little experience with 
>> molecular dynamic code such as Amber and I do not know how to 
>> implement the force field for the molecules I'm interested in. Do you 
>> know a tutorial for force field implementation?
>>
>> Best,
>> Marc Barbry
>>
>> On 5/29/19 5:43 PM, Asmus Ougaard Dohn wrote:
>>> Dear Marc Barbry,
>>>
>>> Thanks for the interest in the ASE QM/MM functionality. I realise 
>>> that the implementation is lacking some documentation and more 
>>> tutorials, apologies. In any case, staying within ASE only for MM 
>>> subsystems, my colleague Gianluca has recently implemented a force 
>>> field for acetonitrile, which also works in QM/MM (see e.g. 
>>> https://wiki.fysik.dtu.dk/ase/dev/tutorials/acn_equil/acn_equil.html). However, 
>>> it is also possible to couple GPAW (and other QM calculators) to 
>>> more general MM subsystems, which then just need an external MM code 
>>> to handle energy and forces internally within the MM subsystem. I'm 
>>> working with colleagues that achieve this using Amber (and it's ASE 
>>> calculator interface), and they can model MM subsystems containing 
>>> both water and a variety of smaller biomolecules, coupled to a QM 
>>> subsystem.
>>>
>>> I'd be happy to help with any issues there might be if you need to 
>>> couple new MM codes. The ASE interface needs some specific methods 
>>> to present the point charges to the QM calculator, and likewise, for 
>>> new QM codes, you need to feed the point charges into their external 
>>> potentials. I think, in a lot of cases, most of it is already there, 
>>> in ASE.
>>>
>>> Currently, we have no automated or tested way of coupling QM and MM 
>>> over covalent bonds, and I don't really know anything about GW, 
>>> sorry. I can see there's also now a force-mixing QM/MM calculator in 
>>> ASE, I don't know anything about that one either.
>>>
>>> Feel free to contact me directly, or continue through here, I'm not 
>>> sure what the best practices for the mailing list are exactly.
>>>
>>> Best,
>>>
>>> Asmus
>>>
>>>
>>> Asmus Ougaard Dohn
>>>
>>> Research Assistant Professor
>>>
>>> Science Institute, University of Iceland
>>>
>>> Phone: +354 831 9337
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>> *From:* gpaw-users-bounces at listserv.fysik.dtu.dk 
>>> <gpaw-users-bounces at listserv.fysik.dtu.dk> on behalf of marc barbry 
>>> via gpaw-users <gpaw-users at listserv.fysik.dtu.dk>
>>> *Sent:* Wednesday, May 29, 2019 3:05 PM
>>> *To:* ase-users at listserv.fysik.dtu.dk; gpaw-users at listserv.fysik.dtu.dk
>>> *Subject:* [gpaw-users] Embedded GW calculations with ASE and GPAW
>>> Dear ASE and GPAW communities,
>>>
>>> I am interested into calculating the energy level of organic 
>>> molecules, taking into account the environment via QM/MM 
>>> calculations. I went through the ASE tutorial on QM/MM method and 
>>> the associated papers and it looks like what I would need. However, 
>>> the ASE implementation seems to focus on water molecule. Is it 
>>> possible to run QM/MM calculations for another environment than 
>>> water? Where could I find some examples?
>>>
>>> Furthermore, I would rather use GW to get the energy level and not 
>>> only DFT. Is it possible to use the embedded method with the GW 
>>> module of GPAW?
>>>
>>> If you know other software that can perform embedded GW calculations 
>>> I would be curious to learn about it. I know that the programs Votca 
>>> and Fiesta provide such method, but they do not come with tutorials 
>>> or are not open-source.
>>>
>>> Thanks in advance,
>>> Marc Barbry
>>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20190531/b58e44d0/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 1alphaMADN.xyz
Type: chemical/x-xyz
Size: 6299 bytes
Desc: not available
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20190531/b58e44d0/attachment-0001.xyz>