MSD of center of mass (linear polymer)

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I have 100 molecules of linear polyethylene (n=15) in my simulation box, and my goal is to find the self-diffusion coefficient of this polymer by using the center of mass. I have two types of atoms: carbon (C) and hydrogen (H). I am looking for another method to determine the self-diffusion coefficient, aside from using compute msd and compute msd/chunk. Could you suggest an alternative approach to obtaining the MSD by center of mass for linear polymers?

Best,

2

Compute msd/chunk is doing exactly what you are asking for. All that is required for that is the correct assignment of molecule ids (may be done with the reset_atoms command, if needed) and then use compute chunk/atom in a corresponding fashion.

Why are you looking for an alternative?

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