[ase-users] LJ parameters for atom types

Wed Nov 6 20:11:26 CET 2019

Dear Asmus,

even changing the input file (adding zeros for H atoms) does not solve the
problem.

In /ase/calculators/qmmm.py

combine_lj_lorenz_berthelot

sigma_c = np.zeros((len(sigmaqm), len(sigmamm[cc])))

sigmamm[cc] is calling a specific element of the list so of course there is
no len() possible.

I changed it now to sigma_c = np.zeros((len(sigmaqm), len(sigmamm))) which
make it work.

However, another error is raising:

  File "/ase/calculators/qmmm.py", line 418, in calculate

    if ~np.any(eps[qa, :]):

TypeError: list indices must be integers or slices, not tuple

Best,

Daria Tombolelli

On Wed, 6 Nov 2019 at 18:14, Asmus Ougaard Dohn <asod at hi.is> wrote:

> Dear Daria,
>
> Your MM LJ input shouldn't be floats, as water has 3 atoms per molecule. I
> know that the eps and sig for the water Hs are 0, but you still have to
> tell that to LJInteractionsGeneral.
>
> So I.e., if the water part of your atoms object is ordered like
> 'OHHOHHOHH...' then your MM Lj arrays should look like: eps_mm = np.array([epsilonOtip3p,
> 0, 0]) and likewise for sig.
>
> Hope that helps.
>
> Best,
>
> Asmus
> ------------------------------
> *From:* Daria Tombolelli <tombolelli.daria at gmail.com>
> *Sent:* Wednesday, November 6, 2019 3:06 PM
> *To:* Asmus Ougaard Dohn <asod at hi.is>; ase-users at listserv.fysik.dtu.dk <
> ase-users at listserv.fysik.dtu.dk>
> *Subject:* Re: [ase-users] LJ parameters for atom types
>
> 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/>
>
>
>
>
>

-- 
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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