MD Simulation with MACE agnesi medium model

[RISHAV01CODER]

Hello everyone,
I ran the following script:

from mace.calculators import mace_mp
from ase import build
from ase.md import Langevin
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase import units

macemp = mace_mp(model="https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0b/mace_agnesi_medium.model") # downlaod the model at the given url
atoms = build.molecule('H2O')
atoms.calc = macemp

T_init = 300 # Initial temperature in K
MaxwellBoltzmannDistribution(atoms, T_init * units.kB)

Set up the Langevin dynamics engine for NVT ensemble.
dyn = Langevin(atoms, 0.5 * units.fs, T_init * units.kB, 0.001)
n_steps = 200 # Number of steps to run
dyn.run(n_steps)

And then got the following output:

"True" it says at the end. So is the MD Simulation complete? And if yes, then how to visualize it? Kindly help.

Thanks and Regards.

[gabor1]

I'm afraid we don't have the capacity to tutor you in using the Atomic Simulation Environment. Please read the documentation here: https://wiki.fysik.dtu.dk/ase/

[RISHAV01CODER]

Yes sir. I discussed your work, MACE model and your task with one of the professors and his PhD students of our department who partly works on modelling and simulations, but unfortunately they aren't working on ML equipped MD Simulations. So, they couldn't really help me much apart from giving me a workstation.
Anyways, I'll go through the documentation of ASE, in depth this time. I am also doing a course on Materials Informatics and Data Science from coursera, halfway through it. Will also look out for some related internship this summer. Maybe then I'll get more familiarised with the outputs. I would like to thank you professor for your time, guidance and bearing with me. Thank you!

[ilyes319]

Hey @RISHAV01CODER, please have a look to our tutorials, it will teach you some ASE basics along the way too:
https://mace-docs.readthedocs.io/en/latest/examples/tutorials.html

[RISHAV01CODER]

Thanks a ton @ilyes319 !

[gabor1]

ASE is not specific to ML, it is a general modeling and simulation package.

[RISHAV01CODER]

Yes sir. Actually, in our lab they are mainly working on FEA and not MD Simulations. But the good part is, I just got the contact of few guys from Biochemical department who work on MD. Will contact them and discuss with them incase any petty doubts not specific to MACE arise. Thank you!