Comparing Membrane Simulations to Scattering Experiments: Introducing the SIMtoEXP Software

Abstract

SIMtoEXP is a software package designed to facilitate the comparison of biomembrane simulations with experimental X-ray and neutron scattering data. It has the following features: (1) Accepts number density profiles from simulations in a standard but flexible format. (2) Calculates the electron density epsilon(z) and neutron scattering length density nu(z) profiles along the z direction (i.e., normal to the membrane) and their respective Fourier transforms (i.e., F ( epsilon )[q ( z )] and F ( nu )[q ( z )]). The resultant four functions are then displayed graphically. (3) Accepts experimental F ( epsilon )(q ( z )) and F ( nu )(q ( z )) data for graphical comparison with simulations. (4) Allows for lipids and other large molecules to be parsed into component groups by the user and calculates the component volumes following Petrache et al. (Biophys J 72:2237-2242, 1997). The software then calculates and displays the contributions of each component group as volume probability profiles, rho(z), as well as the contributions of each component to epsilon(z) and nu(z).