Questions tagged [atomistic-simulation]
An atomistic simulation is a computer simulation method for analyzing the physical movements of atoms and molecules. https://en.wikipedia.org/wiki/Molecular_dynamics
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How to Create a 2D Structure of Boron (Brophene) using ASE?
Unlike Graphene and MoS2, For borophene, I didn't find any inbuilt function in ASE. I have tried to make it, but i failed. So If anyone could help me, it will be great help.
Since brophene has ...
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Python library to obtain atomic orbitals of atoms in the lowest energy state
I want to code an UHF code. Hence for each atom I need the lowest energy electronic configuration. Is there a python package/library that already does it?
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Clustering Algorithms with Periodic Boundary Conditions
I've been working on a project that involves the clustering of data with periodic boundary conditions. Like simulation of extra-framework water species.
Specifically, I am looking for clustering ...
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Thermodynamics: System versus Ensemble
In the context of thermodynamics, an ensemble is a hypothetical collection of identical copies of a system, each in a different state, used to represent the statistical behavior of the system.
That ...
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When should I use Charge-Charge Interactions, Charge-Dipole Interactions, and Dipole-Dipole Interactions in molecular simulation?
I used LJ-potential, Hard-sphere, Soft-sphere, Harmonic, Square-well, etc. potentials in the case of simulation of polymer movement. However, I never used
Charge-Charge Interactions
Charge-Dipole ...
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Are lattice-based Monte Carlo simulations used in the case of liquids and gases?
The Ising model uses a lattice-based model as it is reasonable to simulate magnetic behavior in a solid.
Is lattice-based Monte Carlo modeling used in the case of the simulation of gases and liquids (...
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What factors determine the selection of a specific type of MC move?
There are several types of Monte Carlo (MC) moves that can be used in simulations:
Metropolis-Hastings: a sampling technique used to generate a Markov chain of states with desired probabilities by ...
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What is the minimum number of atoms required to run a Monte Carlo simulation meaningfully?
What is the minimum number of atoms required to run a Monte Carlo simulation meaningfully?
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Copper FCC structure using ASE (Atomic Simulation Environment) library in python
I want to create a FCC structure using ASE (atomic simulation environment). I have define the all the required parameter correctly but at the time when i add GPAW calculator. The output of the program ...
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What are some symptoms that could tell me that my simulation is not running properly?
Suppose, I am running a Monte Carlo simulation of protein folding using harmonic potential, function.
The inner loop of Monte Carlo has 100 iterations, and the outer loop has 1000 iterations.
What are ...
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What are some ways to check if a molecular simulation is running properly?
Suppose, I am running a simulation of protein folding.
What are some techniques, methods, or intuitions that help me to understand whether a simulation is running properly, i.e., it is producing the ...
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What is the purpose of a kinetically resolved activation barrier in cluster-based kinetic Monte Carlo simulations?
I read several papers regarding the use of cluster-based kinetic Monte Carlo (kMC) simulations
They mention the need to use a kinetically resolved activation barrier by averaging over the forward and ...
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NPT Molecular dynamics calculation problem
I am trying to heat up my system from 10K to 300K using the NPT ensemble. But the temperature doesn't reach 300K. What do you think is the problem?
This is my code for the heating part. However, the ...
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Layer detection in a crystal structure
Context
I have two images from a Monte Carlo Basin Hopping where silicon (in yellow) is getting replaced by germanium (in blue). Both have 32 germanium atoms at Si/Ge = 2.5; only the Ge distribution ...
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Restraining a specific bond in eABF simulations in NAMD? [closed]
I am currently running eABF(adaptive biasing) simulation using NAMD. I need to restrain a few terminal C-H bonds in the system. I tried including the additional definition for bond constraints in the ...
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Simulate liquid solvent mobility through a gel polymer electrolyte
I would like to simulate a liquid solvent (such as TEGDME) embedded into a polymeric cage (such as PEGDM). What is the most meaningful approach to estimate transport properties in such a system?
Three ...
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Effect of System Configuration on MD simulation results
Does System Configuration on which we run MD simulation (to obtain a trajectory for the system under investigation) affects the analysis results.
If it does, then could anybody explain me to what ...
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How is temperature changes implemented in a molecular dynamics simulation?
I copied my question to this community as the advice of a user on Physics SE
MD simulations are always associated with a temperature that represents the natural state of a system.
However, some ...
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How to get started modeling liquid crystals? [closed]
I am an experimentalist who is interested in getting hands on experience with how simulations play into our understanding of liquid crystal formation. I have tried to read several reviews on the topic ...
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Perform energy minimization of multiple models of protein-dna complexes
Is there a software/standalone tool that can perform energy minimization of a large number of protein-dna complex models (more than 1000)?
I know of GROMACS or Chimera or the online servers but is ...
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Understanding use of Machine Learning in Multiscale Enhanced Sampling
Multiscale Enhanced Sampling Using Machine Learning
Multiscale enhanced sampling (MSES) allows for enhanced sampling of all-atom protein structures by coupling with the accelerated dynamics of the ...
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What does it mean by a "site" in the case of a CG model?
A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
What does it mean by a "site" in the case of a coarse-grained (CG)...
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Can protein modeling and simulation be used in developing a marketable product? [closed]
As we all know computer science, electrical engineering, etc. knowledge can be used in developing software and electronics/electrical products that can be sold to end-users (B2C).
Can protein modeling ...
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Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins
What are the definitions of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins?
Examples will be highly appreciated.
Also, please, back them up ...
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What do we simulate with molecular simulation of proteins in the theoretical research?
I know that the following can be simulated:
secondary/tertiary structure prediction
protein-surface/protein-protein interaction tests
protein-ligand binding test
I wonder if references or ...
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Interlink among different length scales of simulation and modelling techniques [closed]
I found this figure:
In the following paper:
A Review on Multiscale Modelling and Simulation for Polymer Nanocomposites
However, I am skeptical about its correctness, as this paper is not peer-...
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What is the relationship between periodic boundary and the simulation box?
Suppose, the size of my simulation box is:
Width = 200
Height = 100
Where,
Top-left corner = (0, 0)
Bottom-right corner = (200,100)
Center of the coordinate is at (100, 50)
What would be the size ...
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Why do we even need periodic boundary conditions?
According to Wikipedia -
Periodic boundary conditions (PBCs) are a set of boundary conditions that are often chosen for approximating a large (infinite) system by using a small part called a unit ...
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Molecular MC simulation is not equilibrating [closed]
Suppose, a polymer has N monomers in its chain. I want to simulate its movement using the bead-spring model.
So, I wrote the following program in Python.
Polymer chain simulation with Monte Carlo ...
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What formula should I use to calculate the total energy of a linear polymer chain?
I am using the Bead-spring model to model a polymer chain.
Suppose, the polymer has 3 monomers in its chain:
$$\ce{A1-A2-A3}$$
And,
I can use the following formula to calculate the total Lennard-Jones ...
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Where should I apply the harmonic spring function in the case of polymer simulation? [closed]
I need to simulate the off-lattice movement of a polymer chain in a 3D space using Monte Carlo simulation. Note this is not a simulation of polymer growth; rather this is about polymer movement/motion....
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How should I calculate total potential in a polymer chain?
Suppose, a polymer has 3 monomers in its chain:
$$\ce{A1-A2-A3}$$
When calculating total LJ potential, do I need to calculate like this:
$$E(r_{12})+E(r_{23})+E(r_{31})$$
Or, do I calculate: $$E(r_{12}...
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What does it mean by pruning and enrichment in the case of Rosenbluth method? [closed]
As far as I understand:
Pruning means deleting something.
Enrich means to enhance/increase weight.
Now my question is, in the case of pruned-enriched Rosenbluth method (PERM):
For pruning/enriching, ...
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Polymer simulation [closed]
I am absolutely new to Polymer simulation. I am trying to understand the simulation by analyzing source code written by others.
Can anyone tell me what are the differences between the following three ...
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What are some recent significant developments/studies in theoretical nonlinear chemical dynamics?
During my undergraduate studies, I was introduced to oscillatory and nonlinear reactions, which are essentially chemical reactions oscillating far away from equilibrium conditions - A very visual ...
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How to calculate the surface area of a stepped surface slab in a unit cell? [closed]
I am trying to calculate the surface energies of Ni fcc (111) and (311) surfaces, therefore I need to calculate the surface areas. I use periodic slabs to model these surfaces. For a flat fcc (111) ...
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In which theoretical framework does the size of an atom depend on the temperature of the gas (Bose-Einstein condensates)
In order to pose the question, I reproduce an excerpt from this Physics.SE question, about the size of atoms in a Bose-Einstein condensate (BEC):
Heisenberg's uncertainty principle in frames of ...
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Do we know for sure that all atomic and molecular wavefunctions decay exponentially as r goes to infinity?
Slater type orbitals (STO) are considered to be more accurate than gaussian type orbitals (GTO) for atomic and molecular QM calculations because - among other reasons - they decay with $e^{-\alpha r}$ ...
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How might inclusion of a Grimme dispersion correction influence a simulation of a dense liquid that is not water?
I adapted an example first-principles water simulation to do simulations of liquid SiO2, but did not know what I was doing and did not remove a Grimme dispersion correction term.
It would be great to ...
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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 ...
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elastic constants transformation/basis change P21/a -> P21/n
I just calculated the stiffness tensor for a given material (a monoclinic molecular crystal)
using molecular simulation. When trying to compare my results to published experimental results
I found ...
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Are there any codes to study magnetic materials?
I have used a few codes for studying magnetic materials (specifically core-shell nanoparticles with an AFM shell and an FM core). These are:
Vampire: For the calculation of curie temperature via ...
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How to calculate the exchange matrix of a bilayer magentic system?
I have been using the Vampire atomistic simulation software for a while and it has a useful simulation for predicting the curie temperature. But in order to do that I need the exchange matrix of Co-...
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