Questions tagged [molecular-modeling]
Questions to do with molecular modeling.
79
questions
7
votes
1answer
305 views
Given the adjacency matrix of a molecule, how can I get a graphical representation using only open source software?
In Huckel Method, by numbering the sp2 carbons in a molecule with conjugated double bonds, we can assemble its secular determinant in a form similar to the adjacency matrix of a graph. Taking trans-...
8
votes
1answer
150 views
Calculating compressibility from a molecular dynamics simulation: what is meant by "volume fluctuation"?
I am trying to calculate isothermal compressibility from an NPT molecular dynamics simulation, but am not that experienced and don't know how to use an expression from a paper to do it.
The part that ...
5
votes
4answers
310 views
3
votes
1answer
20 views
Question regarding conflicting results of checking the electron-preciseness of isoelectronic species via NBO and EHM calculations
(Cross-posting from Chemistry.SE due to recommendation that this be posted here; see comment section)
It is well known that the tert-butyl cation's empty 2p orbital on the central carbon is stabilised ...
5
votes
0answers
47 views
How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files?
The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering ...
2
votes
1answer
44 views
Determining the geometry of UOx and WOx for (x=1-3)
Is there a way to work out the geometries for the $\ce{UO_x}$ and $\ce{WO_x}$ species for ($x=1-3$).
I know that deducing the multiplicity (the number of unpaired electrons) in d and f block ...
4
votes
1answer
71 views
Density functional theory and oxygen spin
I would like to perform single-point/geometry-optimization/NEB calculations on systems involving both molecular oxygens and adsorbed oxygens. Reductions by hydrogens are also involved.
I am still ...
6
votes
2answers
159 views
How to find out the multiplicities of molecules containing d and f block species?
I know that the U atom has four unpaired electrons. Therefore it has a total spin S of 2. This means its multiplicity is 2S+1 = 5.
Now consider a complicated molecule such as $UF_6$. In theory all I ...
6
votes
1answer
58 views
What is the polarization catastrophe?
I heard about the polarization catastrophe in a talk about polarizable force fields.
The speaker talked about how the dipole induction is damped at short range to avoid the “polarization catastrophe&...
8
votes
1answer
318 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 &...
7
votes
0answers
63 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
votes
0answers
73 views
References related to the molecular distance geometry problem (estimating true distances based on noisy distances)
One aspect of the molecular distance geometry problem (MDGP) described in this PDF, can be written as follows:
"Given observations of noisy distances between atoms in a molecule, estimate the ...
9
votes
2answers
91 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 ...
7
votes
2answers
97 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_\...
9
votes
2answers
159 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
votes
3answers
108 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
votes
0answers
36 views
Construction of dimeric protein models, selection and refinement [closed]
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 ...
10
votes
1answer
218 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
votes
1answer
57 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 ...
12
votes
1answer
150 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
votes
1answer
55 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
votes
1answer
264 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
votes
1answer
47 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
98 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
votes
2answers
75 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
votes
1answer
121 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 ...
14
votes
1answer
337 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
votes
1answer
99 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
votes
1answer
307 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
votes
0answers
58 views
Should one normalize the "features" in binary fingerprints? [closed]
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
votes
2answers
253 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
votes
1answer
80 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 ...
9
votes
1answer
101 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 1x1x1 box with periodic boundary conditions and with $N = 500$ ...
51
votes
3answers
9k 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
votes
1answer
83 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 ...
12
votes
1answer
89 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
votes
1answer
101 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
votes
1answer
151 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 ...
11
votes
4answers
890 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
2answers
1k 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
votes
3answers
93 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
votes
2answers
105 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
votes
1answer
182 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
votes
1answer
102 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
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 ...
10
votes
1answer
139 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
votes
0answers
62 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
votes
1answer
58 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
246 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
votes
1answer
474 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 ...