Structure Factor Calculations

Calculation of Structure Factors using VMD

The following script is used to calculate the average x-ray or neutron structure factors from a simulation of a lipid bilayer system. The corresponding density profile is also calculated. Errors in the calculated structure factors are also given which can be used to calculate sets of mock structure factors and their corresponding density profiles (via the Box-Muller algorithm) to get error bands on the real space density profiles (calculation not done in the script). See the following reference.

References:

Structure Factor Calculations: Benz, R.W., Castro-Roman, F., Tobias, D.J., White, S.H., Experimental Validation of Molecular Dynamics Simulations of Lipid Bilayers: A New Approach, Biophys. J., 88:805-817. (link)

Script: sfCalc.tcl

Additional Files: sfCalcInp.tcl

Use: After editing the sfCalcInp.tcl file, just execute the script in VMD:

vmd -dispdev text -e sfCalc.tcl

Notes: The user must provide a system file (psf or pdb) as well as a configuration or trajectory, which are specified in the sfCalcInp.tcl file. Other values must also be set in the input file, which is commented and should be straightforward to modify.