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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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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 ...
Md. Jahid Hasan Sagor's user avatar
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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: ...
Md. Jahid Hasan Sagor's user avatar
6 votes
1 answer
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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 ...
Md. Jahid Hasan Sagor's user avatar
4 votes
1 answer
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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 ...
Md. Jahid Hasan Sagor's user avatar
5 votes
1 answer
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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 ...
Pranoy Ray's user avatar
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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 =...
Abdullah Shahriar's user avatar
5 votes
2 answers
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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 ...
Another.Chemist's user avatar
2 votes
1 answer
117 views

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 ...
Pradip Si's user avatar
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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 ...
eraldcoil's user avatar
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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 ...
Akshit Dhillon's user avatar
5 votes
1 answer
342 views

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?
mle's user avatar
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6 votes
1 answer
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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 ...
Saha_1994's user avatar
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4 votes
2 answers
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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 ...
user366312's user avatar
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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 ...
user366312's user avatar
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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 (...
user366312's user avatar
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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 ...
user366312's user avatar
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2 votes
2 answers
140 views

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?
user366312's user avatar
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4 votes
2 answers
314 views

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 ...
Akshit Dhillon's user avatar
2 votes
1 answer
172 views

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 ...
user366312's user avatar
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2 votes
1 answer
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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 ...
user366312's user avatar
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2 votes
1 answer
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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 ...
rmza7's user avatar
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3 votes
1 answer
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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 ...
anumoy ganguly's user avatar
4 votes
1 answer
184 views

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 ...
Saha_1994's user avatar
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2 votes
0 answers
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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 ...
Hemanth Haridas's user avatar
2 votes
0 answers
61 views

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 ...
Marco Di Gennaro's user avatar
3 votes
1 answer
76 views

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 ...
anupama's user avatar
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7 votes
1 answer
338 views

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 ...
Paul's user avatar
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3 votes
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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 ...
Yetinsyny's user avatar
3 votes
1 answer
71 views

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 ...
Lily Sharpton's user avatar
4 votes
1 answer
138 views

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 ...
user366312's user avatar
  • 2,546
2 votes
1 answer
54 views

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)...
user366312's user avatar
  • 2,546
2 votes
0 answers
47 views

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 ...
user366312's user avatar
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4 votes
1 answer
158 views

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 ...
user366312's user avatar
  • 2,546
2 votes
1 answer
104 views

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 ...
user366312's user avatar
  • 2,546
1 vote
0 answers
45 views

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-...
user366312's user avatar
  • 2,546
3 votes
2 answers
167 views

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 ...
user366312's user avatar
  • 2,546
2 votes
1 answer
624 views

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 ...
user366312's user avatar
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3 votes
0 answers
130 views

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 ...
user366312's user avatar
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3 votes
1 answer
80 views

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 ...
user366312's user avatar
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3 votes
1 answer
403 views

Where can I find this formula?

I found this source code written by someone: ...
user366312's user avatar
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4 votes
0 answers
62 views

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....
user366312's user avatar
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3 votes
1 answer
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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}...
user366312's user avatar
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4 votes
0 answers
76 views

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, ...
user366312's user avatar
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1 vote
0 answers
70 views

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 ...
user366312's user avatar
  • 2,546
8 votes
0 answers
93 views

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 ...
mykd's user avatar
  • 2,342
6 votes
0 answers
485 views

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) ...
Shaun Han's user avatar
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9 votes
1 answer
103 views

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 ...
Arc's user avatar
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18 votes
1 answer
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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 $e^{-\alpha r}$ ...
Arc's user avatar
  • 603
9 votes
1 answer
102 views

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 ...
NTS's user avatar
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5 votes
1 answer
66 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 ...
M. Y. Zuo's user avatar
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