Questions tagged [atomistic-simulation]
The atomistic-simulation tag has no usage guidance.
32
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Layer detection in a crystal structure
The situation here, 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 ...
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Restraining a specific bond in eABF simulations in NAMD?
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 ...
- 705
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simulate liquid solvent mobility through 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 system?
Is MD a ...
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1
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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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Av. pressure in NPT equilibration of highly concentrated system
I'm relatively new to MD simulation, and am studying a highly viscous system of very concentrated aqueous biphasic systems of two different electrolytes. The higher-concentration systems are ...
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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?
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 ...
- 31
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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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1
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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 ...
- 1,267
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0
answers
43
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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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3
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2
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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
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1
answer
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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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1
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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 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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84
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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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123
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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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3
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312
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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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