[ase-users] QMMM simulation of metal cation hydration

[Offermans Willem]

Hi Nancy and ASE friends,

I’m not an expert in QMM simulations, but
Atom and Atoms are different objects.
To me, it looks like you cannot combine them with
the + operator.

Probably you need an append atom method of the atoms object.
Maybe the following will help:

https://wiki.fysik.dtu.dk/ase/ase/atoms.html#ase.Atoms.append

B.t.w. I would be very interested in how you will manage to build up your system eventually.



Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,


Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>

[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local]

On 18 Jun 2020, at 23:43, nancy via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>> wrote:

Hi I am a new person to ASE and I am trying to do QMMM simulation of metal cation hydration. I wonder how to build a system like 58 water molecules and 1 Na(+) molecule?

I tried:


from ase.calculators.tip4p import TIP4P, rOH, angleHOH, epsilon0, sigma0

a1 = Atom(’Na', position=[0,0,0], charge = +1)

x = angleHOH * np.pi / 180 / 2
pos = [[0, 0, 0],
       [0, rOH * np.cos(x), rOH * np.sin(x)],
       [0, rOH * np.cos(x), -rOH * np.sin(x)]]
a2 = Atoms('OH2', positions=pos)
vol = ((18.01528 / 6.022140857e23) / (0.9982 / 1e24))**(1 / 3.)
a2.set_cell((vol, vol, vol))
a2.center()
a2 *= 48
a2.set_cell((0,0,0))

atoms = a1 + a2

But this give me TypeError: unsupported operand type(s) for +: 'Atom' and ‘Atoms’

How could I fix it?
Thank you for your help

Best wishes

Nancy
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