Questions tagged [molecular-modeling]

Questions to do with molecular modeling.

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7
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48 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 ...
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51 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 ...
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_\...
7
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0answers
41 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, ...
6
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2answers
55 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
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1answer
202 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 ...
5
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1answer
53 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 ...
11
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1answer
132 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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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 ...
9
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1answer
219 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, $M = {(\ce{O}, R_\ce{O}), (\ce{H}, R_\ce{H}), (\ce{H}, R_\ce{H})}$, ...
5
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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
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1answer
78 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 ...
12
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2answers
66 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 ...
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 ...
13
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1answer
207 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 ...
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 ...
0
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1answer
285 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
52 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?
11
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2answers
203 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 ...
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 ...
7
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1answer
75 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 $N = 500$ ...
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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, ...
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 ...
10
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0answers
44 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 ...
11
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1answer
95 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
146 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 ...
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4answers
695 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
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2answers
852 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....
9
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3answers
87 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 ...
8
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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 ...
15
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1answer
168 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 ...
11
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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
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5answers
1k 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 ...
8
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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"?
5
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0answers
58 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?
7
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1answer
54 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
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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 ...
11
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1answer
340 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 ...
11
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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 ...
9
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0answers
241 views

I wrote a Python code to do MD for a Lennard-Jones fluid but the VACF is wrong: What might be the problem? [closed]

I am trying to write a molecular dynamics simulation for a Lennard-Jones fluid in a box with periodic boundary conditions. The box has no net momentum. I am writing this in python. I have written a ...
6
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0answers
60 views

How do I generate an aluminum force-field for a LAMMPS input file? [closed]

I have been assigned a project on the generation of a force-field of Al (aluminum) for a LAMMPS potential. I have no idea how to proceed and what to do next. Can anyone please let me know how should I ...
14
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1answer
938 views

How to rectify the error “Lost atoms: original 28437 current 3659” in LAMMPS?

I have modeled a complex structure of a protein and a Carbon nano-cone (used as an indenter to the protein) using PACKMOL. The LAMMPS data file of the complex structure consists of 4 atom types (C O N ...
16
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4answers
414 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 ...
5
votes
1answer
91 views

Conductivity Computations of Molecular Wires [closed]

I am interested to compute the conductivity properties of some molecular organic wires in SIESTA. Since I am new in SIESTA, I would appreciate a guide for beginners to this field.
15
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2answers
376 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, ...
12
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1answer
92 views

What is the impact of the orientation of a molecule in cartesian coordinates to molecular properties?

According to my knowledge, each computational chemistry code optimizes a molecule keeping the input orientation of the molecule. The population and spectral analysis is performed on the optimized ...
15
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1answer
101 views

Types of Discrete molecular models

It is often assumed in cheminformatics that molecules with similar physical structure tend to have similar chemical properties [1]. Based on this, our group has used discrete graphs as a model for the ...
9
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0answers
86 views

Is there any literature that systematically analyzes current quantum chemistry algorithms using Big O notation for time and memory cost? [closed]

Big O notation is commonly seen in the papers on novel computational methods. However, only a few of them include rigorous analysis of the algorithm. Is there any literature that summarizes current ...
18
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1answer
351 views

How to optimize zinc oxide bulk structure at certain pressure with LAMMPS

I am trying to simulate the Zinc oxide bulk structure (periodic) at constant pressure(0.0 ~ 20.0 GPa) to observe phase transition with LAMMPS. However, I approached a problem that the fluctuating ...