Questions tagged [molecular-modeling]

Questions to do with molecular modeling.

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9
votes
2answers
53 views

Classes of Graphs used in Chemistry

I am looking for common categories of graphs used in chemistry, for math research I am doing in graph theory. When I write categories, the meaning is not for graphs design or types of design, but for ...
8
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1answer
296 views

I generated Wannier centers but am having trouble understanding how they relate to the atoms in my system: there are more Wannier centers than atoms?

I'm trying to calculate dipole moments from Wannier centers for the first time and there are basics I don't understand and can't figure out from online resources. The software I'm using has a simple &...
17
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2answers
508 views

Materials Modeling with Raspberry Pi?

Does anyone have any knowledge or direction for creating a homemade Beowolf cluster for materials modeling?I would like to be able to run my own "hobby" simulations at home, so a low energy, ...
7
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0answers
57 views

Molecular Structure Vectorization for Computational Quantum Mechanics

What are the different ways that a molecule can be encoded into a vector? My answer to that question would employ machine learning but maybe there are other approaches, perhaps analytical, e.g., graph ...
8
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0answers
56 views

References for the Molecular Distance Geometry Problem

The molecular distance geometry problem (MDGP) consists of two sub-problems: Given observations of noisy distances between atoms in a molecule, estimate the values of the true distances. Given these ...
11
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1answer
133 views

Functional group detection from geometry

I am currently looking for an efficient way to detect common functional groups - that is, characterize whether a molecule is an alcohol, an aromatic compound, etc. - in a larger database consisting of ...
7
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0answers
42 views

Transformation between two different sets of molecular vibrational normal coordinate systems

Lets assume we have $N$ Atoms and we treat them within the Born-Oppenheimer Approximation. We can calculate the adiabatic electronic groundstate potential. Lets assume we observe two local minima, ...
7
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2answers
92 views

What quantity to perform CBS extrapolation on for adsorption/binding energies?

When calculating complete basis set extrapolations for quantities, such as adsorption energies or binding energies, which depend on the difference between three quantities (i.e. $E_\textrm{prop} = E_\...
6
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2answers
59 views

LAMMPS data files, making atom IDs contiguous

I sometimes need to remove atoms from LAMMPS datafiles by hand, removing each row that corresponds to an atomID I want to remove, then decrementing the total atom count. This causes the atom IDs to no ...
6
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0answers
27 views

Construction of dimeric protein models, selection and refinement

I want to perform a molecular docking between a protein of interest and several ligands. This membrane protein has a transmembrane domain composed of an alpha helix structure, which exerts it's ...
9
votes
1answer
204 views

How to calculate the band structure of a protein molecule

I want to calculate the band structure of a protein molecule. How can I do it using Siesta of Gaussian? I am thinking about QE/VASP as the number of atoms are 600 and computationally it is not ...
14
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1answer
102 views

Why are Norm-conserving Pseudopotentials considered so important?

So I am aware that a norm-conserving pseudopotential enforces the conditions that: Inside the cut-off radius, the norm of each pseudo-wavefunction is identical to its corresponding all-electron ...
11
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4answers
714 views

How to make the input generator plugin work in Avogadro 2 on GNU/Linux?

It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18....
7
votes
1answer
46 views

How to calculate the volumetric energy density of a molecule?

I am trying to store hydrogen in a hydrocarbon. The example can be taken as cyclohexane ($\ce{C6H12}$) which is in a hydrogen-rich state. Its hydrogen-lean state is Benzene. I want to calculate the ...
5
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1answer
54 views

What are the more efficient, or easier, methods of handling electromagnetic interactions?

Since metals, metalloids, non-metals, and composites, have differing characteristics, plug-and-play methods, so to speak, would be useful. Also, as it’s well known that a moving electrical field ...
5
votes
1answer
39 views

Bulding host-guest polymer system for molecular dynamics

I'm thinking of running MD simulation of poling process (heating and cooling in external electric field) of host-guest polymer system: organic chromophore in polymer matrix (PMMA or polycarbonate). So,...
11
votes
1answer
97 views

Binding energy calculation for Zn atom on armchair graphene slab?

I am trying to repeat the result of this paper for Zn absorbed on the armchair graphene slab. The relaxed top and side structures are the following: The relaxed structure is almost the same as the ...
9
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1answer
230 views

How can I implement the Cartesian harmonics?

I'm studying the quantum chemistry calculation and now trying to implement the basic methods. For example, given a water molecule, $M = {(\ce{O}, R_\ce{O}), (\ce{H}, R_\ce{H}), (\ce{H}, R_\ce{H})}$, ...
7
votes
1answer
76 views

Normalization condition in evaluating the radial distribution function for a hard-spheres system

I am trying to simulate a 3D hard-spheres in a box system in python. The idea behind this is that I have to create a system in a 1-by-1-by-1 box with periodic boundary conditions and with $N = 500$ ...
11
votes
1answer
82 views

Unable to recreate data for benzene from paper in GROMACS 2020.5

I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
11
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1answer
70 views

Interpret 2D and 3D data from a PubChem summary of organometallic molecule? Can I “flatten” it when showing on a surface?

I need to "build" an organometallic molecule in Blender/Python then represent it resting on a crystal surface. I'm looking at a PubChem summary for Chloroaluminum phthalocyanine and I can ...
50
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3answers
8k views

DeepMind just announced a breakthrough in protein folding, what are the consequences?

There was some recent media reporting about a purported Google breakthrough on applying machine learning techniques to tackle the protein folding problem, as told for example in this news article, ...
12
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2answers
67 views

What are some of the advantages and disadvantages when using shape consistent pseudopotentials as compared to energy consistent pseduopotentials

From the literature as well as the answer to the question What is the meaning of energy-consistent and shape-consistent in the context of pseudopotentials? I can see that the key difference between ...
6
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1answer
95 views

What is the meaning of energy-consistent and shape-consistent in the context of pseudopotentials?

I am trying to use pseudopotentials to model scattering from heavy molecules. However, I am confused by some of the terminologies of pseudopotentials/ECPs: Norm-conserving according to Wikipedia and ...
14
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1answer
243 views

Gaussian-type orbitals vs Slater-type orbitals in terms of computational efficiency

When creating molecular orbitals via the linear combination of atomic orbitals method I am told that Slater orbitals provide a more accurate representation whilst Gaussian orbitals are computationally ...
26
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3answers
304 views

Where is the extended Hückel method (EHM) still used today?

The extended Hückel method (EHM) proved to be very useful through time, but there are better and affordable models today. One interesting thing about the model is the independence of the Hamiltonian ...
0
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1answer
301 views

Has there been any research on the stability of buckminsterfullerene?

C60 can refer to any substance composed of molecules with 60 carbon atoms. Buckminsterfullerene on the other hand is specifically the substance composed of soccer ball shape molecules with 60 carbon ...
7
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0answers
54 views

Should one normalize the “features” in binary fingerprints?

In regression models to predict chemical compounds' activities, fingerprints are often used as features. Should one normalize a fingerprint feature to be in the 0-1 range?
16
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2answers
107 views

Methods for visualising aromaticity

I was wondering what tools there are for visualising aromaticity and anti-aromaticity in molecules, to what quantum chemistry programs they are interfaced, and what other relevant features they have. ...
10
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0answers
45 views

How can one computationally determine the flammability of a molecular system?

I can imagine one aspect of flammability (the ability of a substance to ignite on fire) to include calculating the kinetics and thermodynamics of the reaction of the system with oxygen. This is not ...
26
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1answer
386 views

How accurate are the most accurate calculations?

Taking into account the fact that the theory of quantum gravity does not exist and the QED calculations are not possible for most realistic chemical systems, what levels of accuracy can we expect from ...
11
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2answers
207 views

How to delete a selection with Avogadro2 (Ubuntu 20.x)?

For reason that I did not understand Avogadro has been phased out of Ubuntu 20.x and the available package Avogadro2 is instead another branch of the package, which ...
17
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5answers
2k views

Bond length from infrared spectra?

It's been taught by my lecturer that infrared (IR) spectra are widely used for chemical bonding determination. My question is: is it possible to calculate bond lengths according to the IR spectra? If ...
14
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2answers
110 views

Spin State of Transition Metal complex

What are the best possible methods and available software to compute the spin-state energetics of transition metal complexes?
7
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1answer
76 views

For ergodicity, what is the significance of the R value and slope?

I am calculating MSDs for the first time and have been struggling to find newbie-level resources on understanding them. If anyone could please suggest any resources or provide guidance on how to ...
16
votes
4answers
428 views

Is there a set of updated, comprehensive benchmarks for speed comparison between different quantum chemistry packages?

I've found a page dedicated to quantum chemistry packages benchmarks, on GitHub, qmspeedtest. But most results there are several years old, and so probably outdated. Is there some place where we can ...
9
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1answer
148 views

Computational biology textbook similar to “Computational Materials Science” by June Gunn Lee

I'm looking for a text for computational biology which is similar in structure to a book called Computational Materials Science by June Gunn Lee. In his book, Lee discusses the theory of MD ...
7
votes
2answers
880 views

Why the Open Babel submenu is faded out in Avogadro 2 and I can't optimize geometry in Mint 20?

It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18....
15
votes
1answer
169 views

Is there any reason not to sum the kinetic and potential energy from an NPT simulation to get internal energy?

I would be very grateful for some newbie-level advice from a thermodynamics guru. I ran NPT simulations on a particular system (in CP2K software) to get fluid densities for use in fluid dynamics ...
8
votes
2answers
92 views

Alanine dipeptide trajectories dataset

I was looking for a dataset of alanine dipeptide trajectories. I was wondering whether there is such dataset available or it is unlikely to find one and I should start running molecular dynamics ...
9
votes
3answers
89 views

Which non-commercial softwares can be used to model amorphous carbon?

I have a fair idea of generating and modeling crystalline materials but what non commercial software programs can be used to model amorphous carbon of a specific dimension, say a $6\times6\times6$ Å ...
22
votes
5answers
379 views

What functions other than Gaussians are used for orbital basis sets?

The Gaussian function $\propto\exp((x-a)^2/b)$ with $b>0$ is one of the most common functions used in molecular modelling (e.g. Gaussian type orbitals). What are some examples of applications of ...
8
votes
1answer
123 views

What is the “overcoherence problem” in Ehrenfest dynamics?

I am a novice in Ehrenfest dynamics and would like to know why Ehrenfest dynamics suffers from the "overcoherence problem"?
11
votes
1answer
99 views

Modelling Diffusion of Molecules Through a Physical Barrier

I would like to model the diffusion of various small molecules (e.g. $\ce{O2}$, $\ce{H2O}$, $\ce{MeOH}$, etc.) through polymeric barrier material (e.g. polyethylene, ethylene vinyl alcohol, ...
17
votes
1answer
121 views

Fermi level change in surfaces with adsorbed molecules

In a DFT standard calculation of a solid 3D material (i.e. bulk metal), one of the properties that can be obtained is the Fermi level $E_F$. This feature is related with the required work to add an ...
11
votes
1answer
353 views

What does the Neighbor command do in LAMMPS?

I frequently see LAMMPS codes, and almost all of them have the neighbor 0.5 bin command. I completely studied the LAMMPS manual for the neighbour command and did ...
7
votes
1answer
55 views

Which non-commercial software can be used to dock two proteins?

I need to dock 2 proteins involved in SARS-CoV-2. They are the spike glycoprotein & membrane protein. I need them to be docked as described in the image below. Since there are many docking ...
10
votes
2answers
244 views

What are the factors to consider before docking 2 proteins?

With no background in biological science, I need help with docking 2 proteins together. This issue is with regards to SARS-CoV-2. The 2 proteins are Spike glycoprotein and membrane protein. What are ...
5
votes
0answers
59 views

What is the difference between Ehrenfest dynamics and Born-Oppenheimer Molecular Dynamics? [duplicate]

What is the fundamental difference(s) between Ehrenfest dynamics and Born-Oppenheimer MD? Also, in what situation(s) or case(s) one is preferred than the other one?
11
votes
6answers
1k views

How do I extract a molecular structure from a CIF file?

When I open a CIF file of a crystal structure in a typical molecular editor like Avogadro, then I just see a few symmetry-unique atoms scattered around the unit cell. But I don't see the full molecule ...