MD-SAXS method with nonspherical boundaries

► MD-SAXS method offers a link between SAXS data and atomic structures of proteins. ► The MD-SAXS method was previously limited to spherical condition. ► We extend the method to nonspherical boundary conditions while retaining accuracy. ► The new method can eliminate a number of water molecules in the simulation. ► The method is computationally effective, particularly for elongated proteins.