Small-angle X-ray solution scattering (SAXS) experiments provide information about protein structures in solution, albeit at low resolution. The molecular dynamics (MD)-SAXS method is capable of linking SAXS data and high-resolution atomic structures of proteins including hydrating water molecules. The MD-SAXS method, which was previously limited to spherical boundary conditions, is here extended to nonspherical boundary conditions while retaining accuracy. The method presented here is computationally effective, particularly for elongated proteins, because a number of water molecules can be eliminated compared to the original formulation. (C) 2012 Elsevier B. V. All rights reserved.