Boundary should not "precisely" be around the protein, otherwise some parts of the protein would "feel" other parts via the boundary. In general, if you apply periodic boundary conditions (PBC), take the dimensions as such so the protein would NOT feel the PBC.
Say you have an unfolded protein (or a MD during which a protein unfolds) whose length is about 20 Angstroms, and you use no explicit solvent. You might not want to take the dimension of the box to be smaller they, say, 40 Angstroms. Its just an example. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 10, 2008 at 11:03, Lee Soin <[EMAIL PROTECTED]> wrote: > But the problem is: how to define a boundary? >
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