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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Suggestions for Comparing Basin Hopping Monte Carlo (BHMC) Simulations to Alternative Methods for Low-Energy Configuration Prediction
I'm working on a project focused on modelling crystalline systems (germanosilicate zeolites), where silicon atoms are substituted with germanium atoms. To identify the lowest energy configurations, I'...
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Issue in integrating verlet-list with molecular dynamics code in fortran
(This question is direct copy-paste from Physics SE asked by myself, since I was unaware of Matter Modelling SE.)
I have written the simplest molecular dynamics code with Langevin thermostat in ...
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How to resolve discrepancy between simulated and analytical diffusive particle statistical behaviour in one-dimension?
Assume a scenario where a Brownian particle with diffusion coefficient $D$ is emitted in a 1-D environment from $z=d$, the reflecting wall is at $z=0$, we know analytically that the PDF of such a ...
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Is there any tool/website available by which I can generate VASP input files?
I am familiar with QE input files, but totally new in VASP. I know by using the quantum espresso input generator(https://www.materialscloud.org/work/tools/qeinputgenerator), we can use CIF file
to get ...
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How to make Quantum espresso input file from Vesta?
here is the CIF file of CaCO3 (http://www.crystallography.net/cod/1010962.html). I have opened it using Vesta and get the following data:
...
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What's the temperature of the output electronic properties get from Quantum Espresso/VASP, even if we use 298 K cell info (atom position) as an input?
Normally to prepare input file (structure of materials) for Quantum Espresso/VASP, I searched the corresponding CIF file from this website (http://www.crystallography.net/cod/result.php), after that I ...
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How to get 192 of CeO2 atoms coordinates using Vesta?
Here is the CIF file of CeO2 (http://www.crystallography.net/cod/1562989.html). One of the paper mentioned that they have used 192 CeO2 atoms constructed by 444 primitive cells. To generate the ...
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Which properties can be directly obtained from Electron Charge Density (obtained from CHGCAR in VASP, etc.) and no other info?
The range of properties I have access to are the following:
SPG
Formation Energy per Atom
Total (Relaxed) Energy per Atom
BandGap
Elastic Tensor
Magnetic Moment (OSZICAR & OUTCAR)
Energy above ...
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Creating 1M NaCl solution using PACKMOL
I want to create a 1M NaCl solution in a 1nm X 1nm X 1nm size cell using PACKMOL. So, what should be the NaCl:H2O ratio for this concentration? My calculation is -
1M NaCl = 1 mole NaCl + 1000 mL H2O
=...
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OpenMPI not running under SLURM in UBUNTU with ORCA?
I have ORCA 5.0.4, OpenMPI 4.1.1 and SLURM in UBUNTU 22 in a single PC with 16 threads.
I have setup this pc and, when I run orca alone, openmpi works. But, when I submit orca through slurm, the ...
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How to make a super cell for molecular crystal with PBC
I am trying to build a supercell for molecular crystals from a .cif file. With the ASE package, the supercell has the perfect PBC, but the atom sequence is very random and might be difficult to match ...
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Beginning in molecular simulation world
I want to do a simulation of an atom (type atom is not important) bouncing inside a spherical surface (the material of the surface is not important too) (i.e. starting from an initial velocity, the ...
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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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