Questions tagged [structure]

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

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Obtaining bulk cut structure

I am studying nanoclusters which I have searched DFT energy landscape and data mining was performed. As the next step, I am trying to prepare a few bulk cut structures but I have no experience in it. ...
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8 votes
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How to calculate a structure factor from a radial distribution function?

I have been trying to take an FFT of the radial distribution function to calculate a structure factor. My understanding is this is the same as the regular FFT from the time to frequency domain. The ...
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9 votes
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How do you calculate a radial distribution function on a lattice?

For the radial distribution function $$g(r)=\frac{N(r)}{4\pi r^{2}dr \rho}$$ how do you do the calculation of the volume of the spherical shell in the denominator, $4\pi r^{2} dr$, when the simulation ...
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3 votes
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How to cut a Nano material from a cif file properly

I am not asking which software to use to or how to remove atoms from a supercell. But rather how to decide which part should be removed. Like do I give preference to some surfaces or some particular ...
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5 votes
1 answer
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Do the U values affect structure optimization with the DFT+U simulation to optimize crystal structure?

I am trying to do structure optimization of TiO2, since titanium is a transition metal, I need to use DFT+U to simulate the right band structure, but the electronic band structure would also affect ...
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7 votes
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Where to find organic molecules atomic coordinates

I have found many organic molecule databases, such as PubChem or chEMBL. But they don't provide the atomic coordinates of each atom on the structure. I'm especially interested in organic molecules ...
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4 votes
1 answer
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What ways are there to sort drug molecules into structurally similar groups?

I would like to use a program to automate sorting drug molecules into structurally similar groups. What protocols, or better yet, software, is available to aid this endeavour? For instance, I know one ...
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A structural transformation package? [duplicate]

What are some of the structural (protein) transformation packages available, which can change a bond length, angle or dihedral?
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5 votes
1 answer
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How to convert a hexagonal unit cell to rhombohedral unit cell?

Hexagonal unit cells can be converted to rhombohedral unit cells, and the latter unit cells have fewer atoms. But how can I convert them? Is there any software or codes that are able to do this ...
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7 votes
2 answers
331 views

Geometry optimization with Moller-Plesset MP4

Can we optimize a molecular structure using Moller-Plesset MP4 method on GAUSSIAN software? If yes what keyword do we have to add?
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7 votes
1 answer
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How to determine the more stable configuration between a flat and a buckled monolayer with DFT?

Using first principles methods (quantum espresso code) I would like to find if a monolayer of a material is flat or buckled. Using the van der Waals interaction in the calculation I found that the ...
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10 votes
1 answer
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Can I do a "constrained" geometry optimization in Quantum ESPRESSO, such that certain dopants appear in certain positions even after relaxation?

I am studying the magnetic properties of bulk ZnO, so I am doping it with transition metal elements in order to observe the magnetic spectrum. I replace a Zn atom with a transition metal element at ...
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5 votes
1 answer
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Order of diffraction pattern confusion in XRD experiment

Somewhere I came across this phrase: "expected diffraction angle for first order reflection." With respect to XRD do I take this as a rule of thumb that the diffraction will always be a ...
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9 votes
1 answer
417 views

Where to obtain MOF structures suitable for carrying out DFT simulations?

For bulk and two-dimensional materials, we can download the structures from many databases, such as Materials Project and CMR. Are there also similar databases for MOF (metal-organic framework) ...
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6 votes
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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 ...
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14 votes
1 answer
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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 forces with BSE ...
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8 votes
2 answers
387 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 ...
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11 votes
1 answer
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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 ...
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4 votes
1 answer
87 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' ?
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15 votes
1 answer
101 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 ...
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15 votes
2 answers
400 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(...
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16 votes
1 answer
119 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 ...
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16 votes
1 answer
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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?". ...
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55 votes
7 answers
978 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?
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