Contents
What is the minimum image convention?
The minimum-image convention is a common form of PBC particle bookkeeping in which each individual particle in the simulation interacts with the closest image of the remaining particles in the system. A common application uses PBC to simulate solvated macromolecules in a bath of explicit solvent.
What are periodic boundary conditions used for?
Periodic boundary conditions are often used to simulate a portion of a larger tissue, such that agents exit and enter the simulation space with similar frequencies and there is no flux of agents out of the tissue.
What is periodic boundary conditions in MD simulations?
Periodic boundary conditions (PBC) are used in molecular dynamics simulations to avoid problems with boundary effects caused by finite size, and make the system more like an infinite one, at the cost of possible periodicity effects.
What is periodic mesh?
The Periodic Mesh utility can be used to generate a grid containing rotational and/or translational symmetric boundaries, for example rotating machinery in use with CFD analysis. This utility provides the first two steps needed for the larger process of Periodic Mesh work flow.
What is the minimum image convention for triclinic units?
Minimum image convention for triclinic unit cell. The minimum image convention (MIC), see for example a short note of W. Smith, is often used in molecular dynamics or monte carlo simulations of periodic systems with an orthorhombic unit cell.
When to use the minimum image convention ( mic )?
The minimum image convention (MIC), see for example a short note of W. Smith, is often used in molecular dynamics or monte carlo simulations of periodic systems with an orthorhombic unit cell. For this special case, it is rather trivial to implement the MIC correctly.
Can You generalize orthorhomic cells to triclinic cells?
The naive idea to simply generalize the algorithm for orthorhomic cells to triclinic cells, does not seem to work. I could find this document, which provides some clues, such as the importance of the reduced basis of the lattice vectors, but it does not contain enough details to make a computer implementation.
Can a cubic cell be described as a three dimensional graph?
The lattice points in a cubic unit cell can be described in terms of a three-dimensional graph. Because all three cell-edge lengths are the same in a cubic unit cell, it doesn’t matter what orientation is used for the a, b, and c axes.