All-atom molecular dynamics simulations of crystals present an attractive way to connect crystallography and computational biophysics.  We have recently described benchmark simulations on a variety of small, well-folded proteins whose crystal structures have been determined at room temperature (J. Phys. Chem. B. 114:12811, 2010).  We present here some newer results on a super-cell consisting of 36 unit cells of a short peptide crystal, refined to a model with four water molecules per unit cell.  We find relatively free movement of water molecules through channels between unit cells, such that at any given moment a unit cell may possess as few as 1 and as many as 9 water molecules within its space, yet the average water density agrees in detail with the reported structure.  This system can be used as a test-bed to study ways in which mobile water molecules are modeled in crystallographic refinements.

Bridging the divide: All atom molecular dynamics simulations of protein crystals

243rd National Meeting (2012)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.