Hello, I calculate the density of my lquid in the equilibrated time range of the density-time plots (NPT runs). I use the gro file of these NPT runs for NVT runs to calculate the self diffusion coefficient at the simulated density. Concerning this gro file: Is this taken from the end of the NPT run or the average of the equilibrated time range? Because this is important for the following NVT simulation. Which system size is listed there at the bottom of the output gro file?
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