cylinder: Calculating Density Inside A Cylinder

Calculates density of atoms inside a cylinder as a function of the cylinder height.

Dependencies

cylinder requires you to have groan library installed. You can get groan from here. See also the installation instructions for groan.

Installation

Run make groan=PATH_TO_GROAN to create a binary file cylinder that you can place wherever you want. PATH_TO_GROAN is a path to the directory containing groan library (containing groan.h and libgroan.a).
(Optional) Run make install to copy the the binary file cylinder into ${HOME}/.local/bin.

Options

Usage: cylinder -c GRO_FILE -s SELECTION -p CYLINDER_POSITION [OPTION]...

OPTIONS
-h               print this message and exit
-c STRING        gro file to read
-f STRING        xtc file to read (optional)
-n STRING        ndx file to read (optional, default: index.ndx)
-o STRING        output file (default: cylinder.xvg)
-s STRING        selection of atoms to analyze
-p STRING        selection of atoms defining cylinder position
-x/y/z           direction of the main axis of the cylinder (default: z)
-r FLOAT         radius of the cylinder in nm (default: 2.5)
-e FLOAT         height of the cylinder in nm (default: height of the box in gro file)
-d INTEGER       grid spacing along the specified axis in points per nm (default: 10)

Use the groan selection language specify selections of atoms (flags -s and -p).

Examples

cylinder -c md.gro -f md.xtc -s "name OH" -p Protein -z -r 3.1 -d 20

The program will calculate the average density of atoms named OH (flag -s) from file md.xtc (flag -f) along the main axis of a cylinder that is oriented along the z-axis (flag -z) and has its center positioned in the geometric center of selection Protein (flag -p). The cylinder has a radius of 3.1 nm (flag -r) and a height corresponding to the z-dimension of the simulation box in md.gro. Information about the ndx groups (such as Protein) will be read from index.ndx (default option). Density will be calculated for z-axis slices separated by 0.05 (1/20) nm (flag -d).

The output will be written into cylinder.xvg (default option) and can be visualized using xmgrace (xmgrace cylinder.xvg). cylinder also calculates the average number of atoms inside the entire cylinder and writes this information to the end of the output file.

cylinder -c md.gro -f md.xtc -s "name OH" -p "Protein; Protein; resname POPC" -z -r 3.1 -d 20

Same as above except the cylinder is positioned in the geometric center of Protein in the xy-plane, while on the z-axis, it will be placed in the geometric center of the selection resname POPC.

cylinder -c md.gro -f md.xtc -s "name OH" -p "Protein; Protein; resname POPC" -x -r 3.1 -d 20 -e 5

Same as above except the cylinder is oriented along the x-axis (flag -x) and has a height of 5 nm (flag -e). That means that the density will only be calculated for x-dimension range of -2.5 to 2.5 nm relative to the cylinder center.

Limitations

Assumes that the simulation box is rectangular and that periodic boundary conditions are applied in all three dimensions.

Always uses center of geometry instead of center of mass.