# density

Calculate density along a coordinate.

density [out <filename>] [name <set name>] [delta <resolution>] [x|y|z] [number|mass|charge|electron] [efile <filename>] <mask1> ... <maskN>

`out`

Output file for histogram: relative distances vs. densities for each mask.

`delta`

Resolution, i.e. determines number of slices. (0.25 Å)

`x|y|z`

Coordinate for density calculation. (z)

`number|mass|charge|electron`

Number, mass, partial charge (q) or electron (Ne – q) density. To convert the electron density to e-/Å3 divide by the (average) area spanned by the other two dimensions. (number)

`mask1 ... maskN`

Arbitrary number of masks for atom selection; a dataset is created and the output will contain entries for each mask.

**DataSet Aspects:**

`[avg]`

Average density over coordinate.

`[sd]`

Standard deviation of density over coordinate.

Calculate specified density for system. Defaults are shown in parentheses above. The format of the file is as follows. Comments are lines starting with ’#’ or empty lines. All other lines must contain the atom type followed by an integer number for the electron number. Entries must be separated by spaces or ’=’.

Example input:

density out number_density.dat number delta 0.25 ":POPC@P1" ":POPC@N" \ ":POPC@C2" ":POPC" density out mass_density.dat mass delta 0.25 ":POPC@P1" ":POPC@N" \ ":POPC@C2" ":POPC" density out charge_density.dat charge delta 0.25 ":POPC@P1" ":POPC@N" \ ":POPC@C2" ":POPC" density out electron_density.dat electron delta 0.25 efile Nelec.in \ ":POPC@P1" ":POPC@N" ":POPC@C2" ":POPC" ":TIP3" \ ":POPC | :TIP3" "*" density out ion_density.dat number delta 0.25 ":SOD" ":CLA"

See also $AMBERHOME/AmberTools/test/cpptraj/Test_Density.