Questions tagged [molecular-modeling]
Questions to do with molecular modeling.
49
questions
2
votes
0answers
18 views
Rule of Mixtures calculation
I do not understand a part from rule of mixtures.Particularly between upper bound elastic modulus and lower bound elastic modulus calculations I seriously do not understand what value to choose based ...
12
votes
2answers
126 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 ...
9
votes
0answers
28 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 ...
8
votes
1answer
64 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 $N = 500$ ...
45
votes
2answers
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, ...
8
votes
1answer
57 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 ...
7
votes
0answers
32 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 ...
10
votes
1answer
74 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
137 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 ...
10
votes
3answers
401 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
545 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
76 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 ...
9
votes
2answers
81 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 ...
16
votes
1answer
149 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 ...
12
votes
1answer
88 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, ...
18
votes
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
votes
1answer
110 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"?
6
votes
0answers
52 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?
8
votes
1answer
49 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 ...
11
votes
2answers
241 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
144 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 ...
12
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 ...
10
votes
0answers
113 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 ...
7
votes
0answers
55 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 ...
12
votes
1answer
668 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 ...
17
votes
4answers
348 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
83 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.
16
votes
2answers
353 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, ...
13
votes
1answer
85 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
votes
1answer
95 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 ...
10
votes
0answers
80 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
votes
1answer
285 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 ...
16
votes
1answer
74 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.
...
16
votes
4answers
198 views
Are there any open source software for calculating the rotational and translational entropy of molecules?
What is a good open source software for calculating the rotational and translational entropy of molecules? The National Institute of Standards and Technology does not provide standard molar entropy ...
13
votes
1answer
64 views
Rule-of-thumb for Morse potential cutoff in molecular dynamics?
Is there a rule-of-thumb for selecting a cutoff for the Morse potential in molecular dynamics simulation? For instance, is it typically some multiple of the equilibrium distance?
15
votes
2answers
93 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?
13
votes
1answer
136 views
What are the steps to prepare a surface for molecular adsorption simulations on it?
I want to study the interaction of a given surface with some molecules.
How should I prepare the surface for that kind of simulation?
By prepare the surface I mean how many atom layers, how many of ...
26
votes
1answer
317 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 ...
14
votes
2answers
111 views
What is the largest system for which vibrationally resolved electronic spectra have been simulated using ML-MCTDH?
Multi-layer Multi-configuration time-dependent Hartree (ML-MCTDH) is a method widely used for simulation of vibrationally resolved electronic spectra that incorporate the coupling between vibrational ...
21
votes
5answers
350 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 ...
15
votes
1answer
114 views
Modeling vibronic interaction beyond Born-Oppenheimer
Within Born-Oppenheimer approximation, the motion of atomic nuclei are considered as being separated from the electrons movement. Although in general this approximation is valid for a high number of ...
16
votes
1answer
68 views
Protein cavities - methodological starting point for basic characterization
Characterizing surface properties is important for understanding how proteins execute their function by interacting with other molecules. This includes characterizing cavities. Perhaps the simplest ...
16
votes
2answers
101 views
How to model a random distribution of molecules attached to a surface?
In the same aspect as some of my previous questions, I am interested in modeling molecules on different surfaces and to study the interfacial effect on them.
One of the most important problems that ...
15
votes
2answers
127 views
Convergence by energy and/or density?
The SCF is an iterative procedure to produce the ground state energy and wavefunction for Hartree-Fock, MCSCF, and DFT. Due to the iteration, one needs to establish convergence criteria. Depending on ...
19
votes
3answers
244 views
What software is needed in chemoinformatics or materials modeling, that a solo programmer could work on?
I want to make a pet project in cheminformatics and I need to hear from the community about the actual challenges in chemistry that might be resolved with a digital solution.
I've been working in ...
18
votes
1answer
109 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 ...
14
votes
1answer
69 views
DFT modeling intermolecular interactions
Density Functional Theory based codes evaluate quite successfully intramolecular forces responsible of the atomic bonding. Within this technique one is able to obtain molecular relaxed structures that ...
20
votes
1answer
114 views
Computational tool for identification of activity cliff
Activity cliffs are defined as pairs of similar compounds with substantial differences in activity (Molecular Diversity, 19, 1021–1035 (2015)). Are there computational tools for the identification of ...
8
votes
0answers
99 views
What are the main mathematical approaches to materials modeling? [closed]
What are the main mathematical approaches to materials modeling? This can include both analytical (closed-form) and numerical techniques.
