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

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SUMMARY

The discussion focuses on the implementation of a molecular dynamics (MD) code utilizing the position Verlet algorithm and velocity rescaling for initialization under periodic boundary conditions. A specific line in the integration routine, which updates the variable Mxx, is questioned for its necessity in calculating the diffusion coefficient. The participants suggest that Mxx may serve as a common origin for particle positions, aiding in the analysis of drift. The conversation emphasizes the importance of understanding the role of Mxx in the context of periodic boundary conditions.

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  • Understanding of molecular dynamics simulations
  • Familiarity with the position Verlet algorithm
  • Knowledge of periodic boundary conditions in simulations
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picat
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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.
 
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Hello picat, :welcome:

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.
 

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