Summary of the Scripts

There are several different categories of scripts and programs provided here. They all relate to running and analyzing simulations of (mostly) membrane and membrane/protein systems. A basic summary of these categories is given below. See each section for more details along with the actual scripts.

*Disclaimer: The scripts here are provided as is. While I have tried to debug the code and make the scripts as general as possible, they may contain bugs, incomplete code, assumptions about the input data, etc. Be sure to run appropriate tests with your data when using the scripts.

General Analysis: The set of scripts given here allow one to perform general analyses using VMD. The scripts are based on a modular architecture in which a general analysis code functions as the base and specific analyses are "plugged-in" to it. Many different types of specific analysis scripts are given, and the user can easily extend the framework to his/her specific needs.

Density Restraints: These scripts allow one to restrain specified component-group distribution parameters (distribution mean position and width) to target values in a NAMD simulation. For example, these restraints could be used to restrain the water distribution in a membrane system to the experimentally determined distribution parameters.

Structure Factor Restraints: Like the density restraints, these scripts allow one to restrain the x-ray or neutron structure factors to specified target values in a NAMD simulation. Given the availability of experimental diffraction data, these restraints can be used to restrain the reciprocal-space structure of the system to the experimental reciprocal-space structure.

Structure Factor Calculation: These scripts are used to calculate the average structure factors and corresponding density profiles (with error bars) from a trajectory of a membrane system. The structure factors are calculated on the relative-absolute scale of Wiener and White.

SFGrapher: A simple application written in Cocoa to display and explore diffraction data from membrane systems.

Coarse Grain System: These scripts are used to generate coarse grain lipid, detergent and protein system, based upon the models of Marrink and Sansom. The generated file can be used in Gromacs to run coarse grain simulations.