# Frenkel/Smit: Exercise 10 - MD NVE Code, PBC

• picat
In summary, the conversation discusses the use of a specific step in the integration routine of a MD code for particles in periodic boundary conditions. The purpose of this step is to define particles that are not put back in the box and it may be used to calculate the diffusion coefficient or measure for drift in the initialization of the code. It is suggested to provide the code for better understanding.

## Homework Statement

I am working on a MD code (http://www.acmm.nl/molsim/frenkel_smit/Exercise_10/index.html) which uses the position Verlet algorithm to integrate the equations of motion and a velocity rescaling algorithm for initialization in periodic boundary conditions.

I wondered why they use a specific step in the integration routine (integrate.f)

Mxx(I) = Mxx(I) + Xxx(I) - Rxx(I)
Myy(I) = Myy(I) + Yyy(I) - Ryy(I)
Mzz(I) = Mzz(I) + Zzz(I) - Rzz(I)

to define particles which are not put back in the box (Mxx). Xxx is the current position and Rxx is the old position.

Mxx is not used in any other way in the propagation itself.

2. The attempt at a solution

Is this step needed to calculate the diffusion coefficient in periodic boundary conditions, i.e. to have some kind of common origin? I cannot imagine what else the usage of this step could be. In the initialization Mxx is set to the current position and the differce (Xxx(I) - Rxx(I)) might give a measure for the drift.

Hello picat,

You want us to follow your crumb trail ? Post the code if you think it's relevant.
Otherwise: if this is fortran, Mxx could also be in a common block and be used elsewhere.

## 1. What is the purpose of MD NVE Code in Frenkel/Smit?

The MD NVE Code is used for molecular dynamics simulations in the microcanonical ensemble, meaning that the number of particles, volume, and energy of the system are kept constant. This allows for the study of the dynamics of a system without any external influences.

## 2. What does PBC stand for in Frenkel/Smit?

PBC stands for Periodic Boundary Conditions. This means that the simulation box has periodic boundaries, allowing for the simulation of an infinitely repeating system. This is important for accurately representing the behavior of a system with a finite number of particles.

## 3. How does the MD NVE Code work in Frenkel/Smit?

The MD NVE Code uses algorithms to calculate the forces between particles, based on intermolecular potentials, and then integrates the equations of motion to update the positions and velocities of the particles. This process is repeated over time to simulate the behavior of the system.

## 4. What are some applications of Frenkel/Smit MD NVE Code?

The MD NVE Code in Frenkel/Smit has various applications in the field of molecular simulations, including studying the thermodynamic properties of a system, understanding the behavior of materials under different conditions, and predicting the behavior of biological molecules in a cellular environment.

## 5. How does PBC affect the results of a simulation in Frenkel/Smit?

PBC has a significant impact on the results of a simulation in Frenkel/Smit. It allows for the simulation of larger systems, which can provide more accurate and realistic results. However, it can also introduce artifacts due to the periodicity of the boundaries, which need to be carefully considered and accounted for in the analysis of the simulation data.