How to calculate collective diffusion coefficient in gromacs?

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Arpit Jain

To calculate the collective diffusion coefficient in GROMACS, follow these steps:

Use gmx msd: Calculate the mean squared displacement (MSD) of water molecules.

Calculate collective diffusion: For collective diffusion, analyze the MSD of the entire water group (not individual molecules).

Apply the Einstein relation: Use the formula D=16lim⁡t→∞1N∑i⟨Δri2(t)⟩D = \frac{1}{6} \lim_{t \to \infty} \frac{1}{N} \sum_{i} \langle \Delta r_i^2(t) \rangleD=61limt→∞N1∑i⟨Δri2(t)⟩ to calculate the diffusion from MSD data.

Ensure you're analyzing the water group as a whole to obtain the collective diffusion coefficient.

all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.

Jaffri. Re

Dear Arpit Jain

Thank you very much for your reply. Is this the same as the self-diffusion coefficient? Because this procedure is similar to what I use to calculate the self-diffusion coefficient of water.

Thanks