Questions tagged [molecular-modeling]

Questions to do with molecular modeling.

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8
votes
0answers
43 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
132 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
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3answers
248 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
373 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
71 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
79 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
128 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
86 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, ...
16
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5answers
653 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
100 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
47 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
42 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
234 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 ...
10
votes
1answer
58 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
votes
6answers
918 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
68 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
50 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
497 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 ...
15
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3answers
220 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
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1answer
74 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
votes
2answers
317 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
votes
1answer
81 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
92 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
74 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
231 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 ...
15
votes
1answer
68 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. ...
15
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4answers
181 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 ...
12
votes
1answer
58 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?
12
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2answers
70 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
135 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 ...
22
votes
1answer
206 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
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2answers
109 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
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5answers
318 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 ...
14
votes
1answer
107 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 ...
15
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1answer
65 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 ...
15
votes
2answers
90 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 ...
14
votes
2answers
115 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
233 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 ...
17
votes
1answer
104 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
67 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 ...
19
votes
1answer
109 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
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0answers
98 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.