Questions tagged [structure]

Question relating to structure in materials modeling. Can be on any scale.

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14
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1answer
75 views

How to characterize surface features in proteins?

When looking at the structure of protein domains I notice many of them show a cleft-like structure in the same location (when aligned to each other). What is a recommended way of characterizing these ...
14
votes
2answers
150 views

What are the parameters that need to be calculated to design the structure of a molecule?

Before performing Molecular Dynamics on a co-polymer that doesn't have a ready-to-use structure anywhere, the monomer fragment was built in Avogadro software with 0 net charge, B3LYP theory and 6-31G(...
16
votes
1answer
70 views

When should geometry relaxation not be performed?

My understanding is that geometry relaxation (i.e. letting the nuclei follow the force gradients of the PES until they reach local minima) should usually be performed in order to get the correct ...
16
votes
1answer
35 views

Does the thermal evolution of molecular structures critically affect the validity of the calculated magnetic anisotropy?

This is a particular aspect I'm interested in, from the more generic question "Does the thermal evolution of chemical structures critically affect the validity of the calculated physical properties?". ...
42
votes
6answers
434 views

Is there a database where we can find previously determined geometries of materials?

For small molecules, NIST has a database of experimentally determined geometries here, and ab initio geometries here. I wonder if there is something similar for materials?