Journal of Membrane Biology

, Volume 235, Issue 1, pp 43–50

Comparing Membrane Simulations to Scattering Experiments: Introducing the SIMtoEXP Software


DOI: 10.1007/s00232-010-9254-5

Cite this article as:
Kučerka, N., Katsaras, J. & Nagle, J.F. J Membrane Biol (2010) 235: 43. doi:10.1007/s00232-010-9254-5


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 ε(z) and neutron scattering length density ν(z) profiles along the z direction (i.e., normal to the membrane) and their respective Fourier transforms (i.e., Fε[qz] and Fν[qz]). The resultant four functions are then displayed graphically. (3) Accepts experimental Fε(qz) and Fν(qz) 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, ρ(z), as well as the contributions of each component to ε(z) and ν(z).


MD simulationX-ray scatteringNeutron scatteringComputer software

Copyright information

© Her Majesty the Queen in Right of UK 2010

Authors and Affiliations

  • Norbert Kučerka
    • 1
    • 2
  • John Katsaras
    • 1
    • 3
    • 4
  • John F. Nagle
    • 5
    • 6
  1. 1.Canadian Neutron Beam CentreNational Research CouncilChalk RiverCanada
  2. 2.Department of Physical Chemistry of Drugs, Faculty of PharmacyComenius UniversityBratislavaSlovakia
  3. 3.Guelph-Waterloo Physics Institute and Biophysics Interdepartmental GroupUniversity of GuelphGuelphCanada
  4. 4.Department of PhysicsBrock UniversityCatharinesCanada
  5. 5.Department of PhysicsCarnegie Mellon UniversityPittsburghUSA
  6. 6.Department of Biological SciencesCarnegie Mellon UniversityPittsburghUSA