Input formats

Sassena expects the following files:

One frame of the trajectory as pdb file. This file is used to assign an element to each atom. The element is inferred with some heuristics from the name of the atom rather than looking at the element entry in the pdb file.

The trajectory has to be supplied as dcd file. Sassena does not wrap / unwrap coordinates into the periodic box, so for calculations that concentrate on the dynamics, unwrapped coordinates have to be supplied – and for calculations that concentrate on the structure, wrapped coordinates have to be supplied.

The config file that instructs Sassena which computations to perform has to be a xml file, described elsewhere. By default, Sassena expects this file to be called scatter.xml.

The database contains lists of the scattering properties of the elements: The coherent and incoherent scattering lengths for neutron scattering and the atomic form factors for X-ray scattering.