Periodic Boundaries in Molecular Dynamics Simulations

In summary, periodic boundaries are used in molecular dynamics to simulate large "infinite" particle systems. One way to ensure that the periodic boundary is accurately simulating molecular outcomes for a finite particle system with a large number of atoms is to redo the calculation with double the size system and compare the results.
  • #1
sqljunkey
181
8
In molecular dynamics people use periodic boundaries to confine particles being simulated. I read here that they are used to simulate large "infinite" particle systems. How can I know that the periodic boundary is simulating actual molecular outcomes for a finite particle system that had a large number of atoms?

In other words, is there a way to find how large my particle system has to be to replicate the same outcome that I would get for a periodic system?
 
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  • #2
One thing you can do is let the experiment decide !
 
  • #3
sqljunkey said:
In molecular dynamics people use periodic boundaries to confine particles being simulated. I read here that they are used to simulate large "infinite" particle systems. How can I know that the periodic boundary is simulating actual molecular outcomes for a finite particle system that had a large number of atoms?

In other words, is there a way to find how large my particle system has to be to replicate the same outcome that I would get for a periodic system?
Redo the calculation with double the size system and see how the answers compare.
 

1. What are periodic boundaries in molecular dynamics simulations?

Periodic boundaries refer to the use of a simulation technique in which the edges of the simulation box are connected to each other, creating a continuous, periodic system. This allows for the simulation of larger systems and avoids edge effects that can occur in non-periodic simulations.

2. How do periodic boundaries affect the behavior of molecules in a simulation?

Periodic boundaries can affect the behavior of molecules in a simulation by creating an artificial environment in which molecules can interact with their periodic images. This can lead to different dynamics and thermodynamic properties compared to non-periodic simulations.

3. What are the advantages of using periodic boundaries in molecular dynamics simulations?

The use of periodic boundaries allows for the simulation of larger systems, which can be more representative of real-world conditions. It also avoids edge effects and can improve the accuracy of simulations by reducing finite-size effects.

4. Are there any limitations to using periodic boundaries in molecular dynamics simulations?

One limitation of using periodic boundaries is that it may not accurately capture the behavior of molecules near the edges of the simulation box. Additionally, the choice of periodic boundary conditions may affect the results of the simulation.

5. How do scientists choose the appropriate periodic boundary conditions for their simulations?

The choice of periodic boundary conditions depends on the specific research question and the properties being studied. Some common choices include simple cubic, face-centered cubic, and body-centered cubic boundary conditions. The appropriate conditions should be chosen based on the desired system size, symmetry, and interactions being simulated.

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