From: Hyuntae Na (htna_at_hotmail.com)
Date: Sun Feb 16 2014 - 18:49:00 CST
Is there any guideline for selecting the water box size for variant size of proteins, dna, and so on?
Some might say that 10A from the surface of a protein is enough, and 20A is too costly. However, it is not clear how the water box size is decided. Does the box size depend on the electrostatic cutoff distance (assuming it is 12A)? Is its selection from an experience or from a rationale? I just begin to wonder how it is decided.
Thank you all.
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