Comparing membrane simulations to scattering experiments: Introducing the SIMtoEXP software

Norbert Kučerka; John Katsaras; John F. Nagle

doi:10.1007/s00232-010-9254-5

Comparing membrane simulations to scattering experiments: Introducing the SIMtoEXP software

Norbert Kučerka, John Katsaras, John F. Nagle

Research output: Contribution to journal › Article › peer-review

95 Scopus citations

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 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., F _ε [q _z ] and F _ν [q _z ]). The resultant four functions are then displayed graphically. (3) Accepts experimental F _ε (q _z ) and F _ν (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, ρ(z), as well as the contributions of each component to ε(z) and ν(z).

Original language	English
Pages (from-to)	43-50
Number of pages	8
Journal	Journal of Membrane Biology
Volume	235
Issue number	1
DOIs	https://doi.org/10.1007/s00232-010-9254-5
State	Published - May 2010
Externally published	Yes

Funding

We thank Scott Feller, Jonathan Sachs, Jason Perlmutter and Jeffery Klauda for providing us with simulation data, and Olle Edholm and Frank Heinrich for valuable feedback. N. K. acknowledges partial funding from the Advanced Foods and Materials Network (AFMNet), a Network of Centres of Excellence of Canada. J. F. N. was supported by the U.S. National Institutes of Health, Institute of General Medicine (grant GM44976).

Funders	Funder number
Institute of General Medicine
National Institutes of Health
National Institute of General Medical Sciences	R01GM044976
Advanced Foods and Materials Network
AUTO21 Network of Centres of Excellence

Keywords

Computer software
MD simulation
Neutron scattering
X-ray scattering

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10.1007/s00232-010-9254-5

Cite this

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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 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., F ε [q z ] and F ν [q z ]). The resultant four functions are then displayed graphically. (3) Accepts experimental F ε (q z ) and F ν (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, ρ(z), as well as the contributions of each component to ε(z) and ν(z).",

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Comparing membrane simulations to scattering experiments: Introducing the SIMtoEXP software

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