Comments (4)
NEB requires exact atom-mapping, and obtaining atom-mapped reactant and product geometries (especially when there are multiple molecules in the reactant i.e. a complex) is non-trivial (requires matching stereochemistry, RMSD etc.). AutodE actually side-steps the problem by only using the bond distances of the forming and breaking bond, and then performing "adaptive" constrained optimisations starting from the reactant complex.
The adaptive path is then refined with a NEB if required. The best you can do, at this stage, is to use the first and last point of the adaptive path trajectory. You can find this in the "transition_states" sub-folder which is generated when you call reaction.locate_transition_state()
or reaction.calculate_reaction_profile()
. The file is usually named <hash>_ll_ad_<bond_rearr>_path.xyz
or <hash>_hl_ad_<bond_rearr>_path.xyz
. @t-young31 pls correct me in case I missed something.
from autode.
Hi @KS-spec – you should be able to do that with the following:
import autode as ade
rxn = ade.Reaction("CC=O.[H]N(C)C>>OC(C)(N(C)C)[H]", name="enamine_1")
rxn.find_lowest_energy_conformers()
rnx.optimise_reacs_prods()
for molecule in rxn.reacs + rnx.prods:
molecule.print_xyz_file()
from autode.
Thank you very much for your kind reply.
The method you provided gave me the coordinates of each of the three molecules separately.
I'd like to get the first and last coordinate of a trajectory such as the below coordinate (1 and 2) before conducting NEB.
Could you please tell me if there is any way to do so?
from autode.
Thank you very much for your reply.
from autode.
Related Issues (20)
- v1.4.0 release
- How to use a wrapper of ase-calculator? HOT 2
- Can't Extract the Hessian from a Gaussian16 calculation HOT 4
- Could not get energy HOT 2
- A new feature for the calculation of thermochemical contributions
- ImportError: cannot import name 'cached_property' from 'functools' HOT 2
- Temperature should be a value
- Better optimisers for NEB
- Performing NEB given exact atom-mapping HOT 5
- Diffrence in frequencies from ORCA and autode HOT 5
- Optimiser bugs
- Implement image-pair regeneration with DHS (-GS) and i-EIP
- Increase default SCF cycles in Q-Chem HOT 2
- SMILES input -> molecule bug HOT 3
- Turn of truncation of structure HOT 2
- DIC->Cart iterative back-transform did not converge HOT 6
- Failed to create a complete set of delocalised internal coordinates HOT 3
- ORCA error ? CouldNotGetProperty: Could not get energy HOT 2
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from autode.