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Questions tagged [structure]

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

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Protein structure prediction: levels of coarse-graining in deep learning approaches

I am researching the areas of protein structure prediction, protein + ligand pose prediction, and co-folding algos with deep learning. I am trying to map the current state of the art architectures ...
operator's user avatar
9 votes
0 answers
70 views

Software recommendation for drawing atomic structures

Anyone familiar what kind of software is used for drawing the atomic strucutres shown in the attached figure?
Jaafar Mehrez's user avatar
2 votes
1 answer
35 views

How to parse GDB SMI file?

Reymond Research Group from Bern University has created [GDB-17][1], a compendium of molecules in SMILES format. The file is in smi format, how do I parse the molecular structure in xyz from this?
ananta's user avatar
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4 votes
2 answers
91 views

Given a .gro file of a monomer, how to polymerize it?

I have a structure (.gro) file of a PolyEthylene Glycol (PEG) molecule as shown below. How do I get the corresponding structure file for PEG-20 i.e., a molecule with a degree of polymerization=20, ...
Pranoy Ray's user avatar
  • 1,635
3 votes
0 answers
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Obtaining RDF from provided structure factor

I have a test structure factor dataset from water O-O pairs and I am trying to get the $g_{OO}(r)$. ...
mykd's user avatar
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8 votes
2 answers
174 views

Linear interpolation between two molecular structures in internal coordinates

I wonder if there is a tool to generate geometries (structures) corresponding to linear interpolation between two structures in internal coordinates, with the two structures being specified in ...
EvGeniy's user avatar
  • 371
3 votes
1 answer
132 views

How to convert a SMILES into a LAMMPS or GROMACS input file?

Are there any dedicated Python tools/packages/scripts that help me convert a SMILES structure into an MD coordinate and topology file (both for GROMACS and just the single one for LAMMPS)? Demonstrate ...
Pranoy Ray's user avatar
  • 1,635
3 votes
0 answers
32 views

Which is the best way to plot E_tot vs Lattice graph for structures with two lattice parameters?

I made the graph using the ratio between the parameters x E_tot (trigonal structure), but I would like to know if there is a better way to do this.
Gabriel Elyas's user avatar
6 votes
1 answer
142 views

Can radial distribution function determine where the interactions of reference (atom/molecule) reduces greatly with surrounding atoms/molecules?

By plotting the RDF (radial distribution function), is it possible to determine at what radius the interactions of surrounding atoms/molecules with the reference atom/molecule reduce greatly? My ...
Night Shade's user avatar
2 votes
0 answers
27 views

How to define the space group of a new material?

I am preparing the following strcture of CdAlCRO4 using Material Studio to further study its properties. However, I am facing difficulty in deciding the space group it belongs to. How to find the ...
Habib Arshad's user avatar
11 votes
1 answer
373 views

Inconsistencies in a famous point group table

The original resource "Tables for Group Theory" By Peter Atkins, Mark Child and Courtenay Phillips (1970). I have been using this 2008 version, in which Pg. 37 has the following table: Some ...
Nike Dattani - No Free Time's user avatar
3 votes
1 answer
508 views

Noob Question: How can I write bulk, monolayer and bilayer structure in input file for visualizing it

I'm getting my bachelor degree in physics and in my structure of matter course we never talked about bulk, monolayer and so on. I can understand Bravais lattice , reciprocal lattice and so on but I'm ...
CoolerThanACooler's user avatar
3 votes
0 answers
44 views

How to draw multiple Lewis structures from the same molecular formula?

I am learning about Lewis octet theory and the following formulae were shown as guidelines to draw Lewis structures: $$ \begin{align} V &= \text{total valence electrons}\\ R &= \text{required ...
ananta's user avatar
  • 221
3 votes
1 answer
579 views

Why the relaxation of my material in Quantum ESPRESSO wasn't achieved?

I did a vc-relax calculation using HSE by Quantum ESPRESSO and after 22h time WALL the job was complete and JOB DONE was mentionned in the end of the output file ...
Camilla's user avatar
  • 2,169
5 votes
1 answer
69 views

Is there a program to compare different structures?

I am looking for a program that can compare different structures and determine if they are equal or not. After performing DFT calculations, the obtained structures may be identical but for reasons ...
leire's user avatar
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8 votes
1 answer
403 views

Do I have to use the same functional for dielectric function calculations, as the one used for relaxing the structure?

This is a general question regarding the practices of doing optical calculations and the role of the ionic contribution to the dielectric function (with heavy reference to VASP). Based on VASP's ...
CW Tan's user avatar
  • 1,316
6 votes
1 answer
90 views

Are all molecules under the same peak in g(r) always found in the same solvation shell?

For a liquid, the peaks in $g(r)$ are typically associated with the solvation shells: nearest neighbors, next-nearest neighbors, and so on. However, the $g(r)$ is averaging over many configurations, ...
user avatar
4 votes
1 answer
123 views

How to generate a polymer in different conformations?

I want to run MD simulations of a polymer, but I want to start from different physical conformations. My question is, how do I obtain these conformations? Is there a software which performs this? Let'...
megamence's user avatar
  • 4,171
4 votes
0 answers
59 views

How are bulk cut structures obtained? [closed]

I am studying nanoclusters in which I have searched the 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 ...
DGKang's user avatar
  • 900
9 votes
1 answer
3k views

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 ...
user avatar
9 votes
1 answer
352 views

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 ...
user avatar
3 votes
0 answers
47 views

How to cut a Nano material from a cif file properly [closed]

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 ...
Parmeet Singh EP 066's user avatar
8 votes
1 answer
607 views

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 ...
Jack's user avatar
  • 2,057
8 votes
1 answer
849 views

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 ...
Carlos Andrés del Valle's user avatar
4 votes
1 answer
76 views

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 ...
Wesley's user avatar
  • 1,040
4 votes
0 answers
68 views

A structural transformation package? [duplicate]

What are some of the structural (protein) transformation packages available, which can change a bond length, angle or dihedral?
BND's user avatar
  • 1,341
5 votes
1 answer
419 views

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 ...
nujabse's user avatar
  • 93
6 votes
2 answers
737 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?
sarra6's user avatar
  • 579
7 votes
1 answer
81 views

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 ...
hakou elhaj's user avatar
10 votes
1 answer
956 views

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 ...
ABDELHAMID AIT MHID's user avatar
5 votes
1 answer
5k views

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 ...
user586228's user avatar
10 votes
1 answer
1k 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) ...
Jack's user avatar
  • 15.2k
6 votes
0 answers
108 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 ...
BND's user avatar
  • 1,341
14 votes
1 answer
296 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 forces with BSE ...
Xiaoming Wang's user avatar
8 votes
2 answers
962 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 ...
gogo's user avatar
  • 1,247
12 votes
1 answer
416 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 ...
Shafayet Rahat's user avatar
4 votes
1 answer
108 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' ?
Alfred's user avatar
  • 1,939
15 votes
1 answer
109 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 ...
Ivan's user avatar
  • 879
15 votes
2 answers
877 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(...
Kavya Mrudula's user avatar
16 votes
1 answer
334 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 ...
2ndQuantized's user avatar
  • 1,021
16 votes
1 answer
48 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?". ...
agaitaarino's user avatar
  • 1,501
57 votes
7 answers
2k 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?
Nike Dattani - No Free Time's user avatar