Comments (4)
Dear @t-s-hofer Thomas:
Thanks for your interest. Yes, we do have an implementation of periodic boundary conditions and you could use it. However, there is no separate “periodic version of the ANI-NPP”. ANI is a rather short-range method and we use a neighbor list to check whether atoms are in cutoff distance or not. So we just use ASE PBC functionality to correctly account for periodicity and feed it into a neural network. As soon as the box larger than a cutoff distance there should be no problems.
I should also note, that public ANI was trained only to isolated organic molecules, do not expect good accuracy for crystals or liquids yet:)
from ase_ani.
Hello,
Thanks for the quick reply and the information. So I take it that pbc is in principle always active, if the respective periodic cell definition is provided in ASE. So no further actions are required in the ANI-NPP files to work with periodicity.
Thank you also for the note on the parametrisation to neutral organic molecules in vacuum. We will be aware to properly benchmark the systems to periodic DFT.
One question to a related topic: Is it safe to treat charged system using ANI-1, e.g. NH4+ or charged aminoacids like glutamate or histidine? Based on the example movie on your github page I assume that there are several charged aminoacid sidechains in the shown protein.
Kind regards,
Thomas
from ase_ani.
@t-s-hofer: this is a development prototype with long-range electrostatics and substantial extra training data. It's not yet published. The public model should work with zwitterions, as soon as the total charge is zero. Isolated ions are likely wrong:/
from ase_ani.
Thanks again for the quick response. The information will help us in implementing the ANI-1 in our routines and in system selection.
I guess this solved and the thread can be closed.
Kind regards,
Thomas
from ase_ani.
Related Issues (20)
- wB97 single vs double precision? HOT 1
- Clarification on training the model HOT 2
- Cuda 9.1/9.2 support HOT 8
- Portable version? HOT 15
- Would angluar shifts from 0 to +pi be sufficient? HOT 2
- geometry optimization doesn't work HOT 1
- problem installing ASED3 HOT 4
- libAEV.so can not open HOT 2
- What is 'default_neighborlist' method in aev.py doing? HOT 3
- computing energy of a benzene crystal results in a RuntimeError HOT 7
- Example of generating the feature vector from a geometry HOT 1
- `ani_quicktest.py` example requires changes to script HOT 4
- Libraries for OpenMM-ANI HOT 2
- libAtomicNNP.so: undefined symbol HOT 1
- ANI-2X
- Import Error: cannot open shared object file: No such file or directory HOT 5
- Problem excecuting ani_quicktest.py with Geforce RTX 3080 HOT 6
- ANI-2x training data set
- Inclusion of Point Charge HOT 1
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