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Results tagged with geometry
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user 1380
Questions about molecular or lattice geometry.
6
votes
1
answer
101
views
Hessian used for calculating GDIIS error vectors
GDIIS (Geometry optimisation with Direct Inversion of Iterative Subspace) is a well known method used by many QM codes for geometry optimisation. … Then the procedure involves minimizing $\sum c_i e_i$ with some constraints, and after some maths, GDIIS generates the new geometry guess $x_{i+1}$. …
- 7,171
10
votes
Accepted
Functional group detection from geometry
You can probably do it with only OpenBabel or RDKit using SMARTS search strings, but you can get a much easier solution if you combine OpenBabel with checkmol (which you have mentioned in the question …
- 7,171
3
votes
1
answer
103
views
Cubic spline interpolation through a series of images
Cubic spline interpolation is used in a lot of methods like Nudged Elastic Band (NEB), or String or Growing String Method (GSM) either to reparameterize the path, or to estimate the position of the pe …
- 7,171
5
votes
Accepted
Gaussian 16: Relaxed scan using Jacobi coordinates expressed using generalized internal coor...
Based on the GIC page in Gaussian website and your picture, the definition of the coordinates would be:
comX = (X(A)*mA + X(B)*mB)/(mA+mB) # these are the cartesian components
comY = (Y(A)*mA + Y(B)* …
- 7,171
4
votes
0
answers
104
views
Is it possible to generate atom-mapped xyz files from reaction SMILES for NEB?
There are SMILES that represent reactions happening (e.g. C=C.O>>CCO representing water addition to ethylene). And I know that there are atom-mapping softwares available from molecule sketchers (ChemA …
- 7,171