Rearding msd calculation

LAMMPS
1

Dear Sir,

In my simulation box, water molecules, polymer and graphene sheet. I want to calculate msd of water molecules only near the graphene sheet. For this, what should I do?

2

This is an ill-defined calculation. Let’s disregard syntax and implementation details and just look at the theory. MSD is looking at the infinite time limit of motion and the Einstein relation states that the MSD will grow linearly in that limit. But with a geometrical restriction (i.e. near the graphene sheet), you have to make a choice which particles to include. There are multiple cases to consider:

  • particles that start within the selected space
  • particles that enter the selected space
  • particles that remain within the selected space

Now for particles that do not remain within the selected space, part of the calculation is invalid since you are looking at behavior outside that space.
And for particles that remain within the space all the time, you have a bias toward immobility.

3

Thanks Sir