Questions tagged [atomistic-simulation]

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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?

I know some: Secondary structure prediction Tertiary structure prediction protein-surface interaction test protein-protein interaction test protein-ligand binding test What else do we simulate? ...
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Interlink among different length scales of simulation and modelling techniques

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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Open issues in MC protein simulation?

What are some open issues in Monte Carlo protein simulation research? I am especially interested in coarse-graining.
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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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2 votes
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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

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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1 answer
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Where can I find this formula?

I found this source code written by someone: ...
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Where should I apply the harmonic spring function in the case of polymer simulation?

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?

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

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?

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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13 votes
3 answers
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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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9 votes
1 answer
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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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