Questions tagged [structure]
Question relating to structure in materials modeling. Can be on any scale.
10
questions
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0answers
78 views
Is this statement correct: “All structural variations are energy driven”? [closed]
In modelling using molecular mechanics can one state that "all structural variations are energy driven?".
The statement is related to protein-ligand binding in modelling.
Sometimes one can ...
10
votes
0answers
84 views
Is there a software that has implemented forces of TDDFT calculations for solids?
I'd like to investigate the structural relaxations of the excited state for periodic systems. BSE and TDDFT are two promising methods for this purpose. While there is a discussion on BSE Is there a ...
8
votes
2answers
67 views
Tools for structural analysis on LAMMPS trajectories
I have a very general question but still quite important since I didn't find convincing tools to get the structural analysis done for LAMMPS dump file (trajectories). I am looking for post processing ...
8
votes
0answers
111 views
How do I predict the structure of a nanoparticle with Calypso and Quantum ESPRESSO?
I want to create a nanoparticle of CuO and predict it's structure. I've done unit cell relaxation with Quantum ESPRESSO. One tool to predict nanocluster structure is Calypso which is PSO-based. I'm ...
4
votes
1answer
75 views
How much energy difference could be used to distinguish optimized results from different initial geometries for the same structure?
Is there a threshold? Could I say that my final geometries are the same with 'energy difference = 0.05 meV/atom' ?
14
votes
1answer
78 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
160 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
76 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
37 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?". ...
47
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6answers
543 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?
