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Partial Solvation by Explicit Water Molecules

When water molecules are included in the simulation, constant-dielectric (CDIE) electrostatics should be employed. For systems of finite size (e.g., a protein hydrated in vacuum), spherical cutoffs are used. Good numerical input values are CTOFnb $\ge 12$ (Å), CUTNb $=$ CTOFnb $+$ 2, and INBFreq $= -1$. Electrostatic SHIFting does not monotonically damp the $1/r^2$ force, but force shifting (FSHIft) and force switching (FSWItch) do. If the system simulated is composed entirely of neutral groups, force shifting (ATOM FSHIft) is the better of the two. As the number of charged groups in the system increases (e.g., hydrated protein), force switching (ATOM FSWItch) is recommended with CTONnb $=$ CTOFnb $-$ 4.

Peter J. Steinbach 2010-11-15