[ase-users] LJ parameters for atom types

[Daria Tombolelli]

Dear Asmus Dohn,

I tried to use the class you suggested me LJInteractionsGeneral but I
encountered a problem.

For now my system is a CO in water where CO is the qm part and waters are
the mm part.

I wanted then to insert different LJ parameters for O of CO and O of water.

This is my input statement for LJ parameters:

interaction =
LJInteractionsGeneral(sigmaqm=(sigmaOM,sigmaCM),epsilonqm=(epsilonOM,epsilonCM),epsilonmm
= epsilonOtip3p,sigmamm=sigmaOtip3p,qm_molecule_size=2)

where OM is for Oxygen of CO, CM is for Carbon of CO.

The problem raise when the function combine_lj_lorenz_berthelot is called
at line 332
sigma_c = np.zeros((len(sigmaqm), len(sigmamm[cc])))

since my sigmamm[cc] is a float (and it has no len()).

I solved changing this line to:
sigma_c = np.zeros((len(sigmaqm), 1))

but I am not sure this is correct.

It would be really nice if you would be able to help me.

Best regards,
Daria Tombolelli




On Wed, 23 Oct 2019 at 11:22, Asmus Ougaard Dohn <asod at hi.is> wrote:

> Hello Daria,
>
> Not silly questions!
>
> If you need to insert different LJ parameters for different atom types of
> the same element, you need to use the LJInteractionsGeneral class
> instead. Apologies for the lack of documentation of that one, we need to
> get that fixed. This calculator simply takes in epsilon/sigma arrays of
> length qm_molecule_size for the qm subsystem and of length mm_molecule_size
> of the mm subsystem and combines them using the Lorenz-Berthelot rules. So
> with that class you have full control of which atom(type)s get which
> parameters.
>
> Second question: Yes.
>
> Addendum: I've made some tools of automatically assigning LJ parameters
> that could maybe come in handy for larger systems, you can find them here:
> https://gitlab.com/asod/aseambertools  . It uses AmberTools for atom
> typing.
>
> Best,
>
> Asmus
>
> ------------------------------
> *From:* ase-users-bounces at listserv.fysik.dtu.dk <
> ase-users-bounces at listserv.fysik.dtu.dk> on behalf of Daria Tombolelli
> via ase-users <ase-users at listserv.fysik.dtu.dk>
> *Sent:* Wednesday, October 23, 2019 8:52 AM
> *To:* ase-users at listserv.fysik.dtu.dk <ase-users at listserv.fysik.dtu.dk>
> *Subject:* [ase-users] LJ parameters for atom types
>
> Hi everyone,
>
> I am trying to use the QM/MM calculator (EIQMMM) for simple calculations
> of i.e. CO in water box, but I don't find anywhere the information about
> how to insert different LJ epsilon and sigma values for different atom
> types, in this case the Oxygen of CO and the Oxygen of water molecules. Is
> this is not possible without using interfaces to other (external) MM
> calculators?
>
> The second question is about the molecular_size parameter in the Embedding
> class: i.e I did a simple QM/MM calculation of water dimer in a water box
> and I left this value to 3. Is it correct?
>
> Sorry for the maybe silly questions and thank you for your help.
>
> Daria
>
> --
> Dr. Daria Tombolelli
> Technische Universität Berlin
> Fakultät II
> Institut für Chemie
> Sekretariat PC 14
> Straße des 17. Juni 135
> 10623 Berlin
>
> E-Mail: daria.tombolelli(at)tu-berlin.de
>
> <http://it.linkedin.com/in/dariatombolelli1987>
> Researchgate <https://www.researchgate.net/profile/Daria_Tombolelli>
>
> Raum: SE-RH 108
>
> wiss. Mitarbeiterin in der Arbeitsgruppe Prof. Dr. M. Mroginski
> http://www.modeling.tu-berlin.de
> <http://www.modeling.tu-berlin.de/menue/modellierung_biomolekularer_systeme/>
>
>
>
>
>

-- 
Dr. Daria Tombolelli
Technische Universität Berlin
Fakultät II
Institut für Chemie
Sekretariat PC 14
Straße des 17. Juni 135
10623 Berlin

E-Mail: daria.tombolelli(at)tu-berlin.de

<http://it.linkedin.com/in/dariatombolelli1987>
Researchgate <https://www.researchgate.net/profile/Daria_Tombolelli>

Raum: SE-RH 108

wiss. Mitarbeiterin in der Arbeitsgruppe Prof. Dr. M. Mroginski
http://www.modeling.tu-berlin.de
<http://www.modeling.tu-berlin.de/menue/modellierung_biomolekularer_systeme/>
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