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The average box sizes determined from this trajectory are used in all subsequent canonical (NVT) trajectories at the same temperature.
We used a minimum box size of 5, with 50 box sizes linearly spaced on a logarithmic scale up to a maximum box size of 1 / 10 of the length of the IAI sequence [50].
However, for larger box sizes the exponents are closer to 0.5 suggesting that the correlations do not extend across these larger box sizes.
Each gray square corresponds to one PDB-bench ligand with the default and optimized box sizes represented by their volumes.
All box sizes = 23 × 23 nm.
For box size 10 the hybrid converges almost ten times faster while for larger box sizes the asset is even more pronounced.
Box sizes correspond to the number of focus molecules and the color intensity is the –log p-value).
Box sizes can be a variety of sizes, so use the measurements as a simple guide.
Keep it tight – airtight … Box Sized Die by João Onofre.
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CEO of Professional Science Editing for Scientists @ prosciediting.com