AMBER Archive (2009)

Subject: [AMBER] Restraining counterions?

From: Francesco Pietra (
Date: Tue Apr 28 2009 - 12:32:18 CDT

A small doubt. During the restrained preliminary procedures (density
equilibration, heating) with a protein in a hydrated lipidic membrane,
and an extra layer of water, are Na+ counterions (added to neutralize
the protein charges) to be treated as WAT, i.e. never restrained? Some
Na+ are inside the hydrated lipidic layer, others in the surrounding
water layer (positioned by leap'd "addions").

francesco pietra

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