Tools specifically intended for analyzing lipid bilayers and related systems, found in the Tools/ directory:
Compute the probability distribution of crossing angles and torsions for a set of chains.
Loop over a trajectory and compute the number waters crossing a membrane.
Construct the density of some membrane component around a protein, as a function of lateral and vertical distance
Calculate the membrane thickness as a function of lateral distance from a protein
Compute the charge/electron/mass density distribution for the system along the z-axis. Produces the distribution for the whole system and an arbitrary number of selections. Requires a structure file format which supplies mass and/or charge. The newest version also has an option to symmetrize the density distribution in z. This assumes that the input trajectory has already been set up with the membrane center at z=0. You can accomplish this using merge-traj, which can optionally recenter a selection at every frame. The functionality from density-dist-windowed has also been folded in, using the –window option. Note: this tool can be used in combination with potential_profile.py to compute electrostatic potentials along the membrane normal.
Compute the charge/electron/mass density distribution for the system along the z-axis for blocks of time within a trajectory, producing a density distribution time series. This is deprecated, since the functionality has been merged into density-dist.
Calculates molecular order parameters, binned by lateral distance from a target.
Calculates a molecular order parameter (using the principal axes of a selection). Used for comparing order between coarse grained and all atom MD.
Compute the distribution of a variety of membrane properties about a membrane properties. Properties currently implemented include height, density, molecular order parameter, and average vector orientation.
Compute the deuterium quadrupolar splitting order parameters for lipid molecules. The model file must have connectivity information. The current version supports both 3 residues/lipid and 1 residue/lipid topology files, and can optionally compute order parameters relative to the x and y axes. In addition, a more careful estimate of statistical uncertainties is available using block averaging.
If you wish to use block averaging to estimate the errors, we suggest running the tool twice: the first time will give you the block standard error as a function of block size, and you can read out the true standard error as the plateau value at large block size. Because the plateau region is often noisy (since the number of blocks is getting small), the code offers you the ability to estimate the plateau value by averaging over a range of numbers of blocks. This defaults to using the estimates from 2 blocks through 5 blocks, but you should check the plots yourself to make sure this is appropriate for your data set. For more on block averaging, see the review by Grossfield and Zuckerman, "Quantifying uncertainty and sampling quality in biomolecular simulations", Annual Reports in Computational Chemistry, 2009, 5, 23-48.
Compute the electrostatic potential profile along the membrane normal. This program takes the output of the density-dist tool run in "charge" mode and returns the electrostatic potential in Volts. The algorithm used here is described by Sachs, et al, J Chem Phys, 2004, 121, 10847, and includes a correction to ensure that the electrostatic potential is continuous at the periodic boundary. A typical command line would look like:
density-dist –type=charge – path/to/model-file path/to/trajectory -38 38 76 > charge-density.dat potential_profile.py charge-density.dat > potential.dat
See the –fullhelp message for more details about the meaning of specific columns in the output.
Note: this tool requires the python numpy extension in order to run.
Computes an area profile along the Z-axis by binning the structure and calcuating the radius of gyration (or max radius) for each bin.
Compute a two dimension radial distribution function in the xy plane, splitting the system into upper and lower leaflets. Primarily intended for analyzing lateral organization of lipid-water interfaces. Note that as of version 1.6.0, the command line arguments have changed significantly. The new version allows you control how your selection is split up, by residue, segment ID, or molecule (if your system file has connectivity).
Same as xy_rdf, except producing a series of block averages rather than averaging over the whole trajectory. This program is deprecated, because its functionality has been merged into xy_rdf.