Calculate the distance between two points.

distance [<name>] <mask1> [<mask2>] [point <x> <y> <z> ] [ reference | ref | refindex <#> ] [out <filename> ] [geom] [noimage] [type noe]

Options for ’type noe’:
[bound <lower> bound <upper>] [rexp <expected>] [noe_strong] [noe_medium] [noe_weak]
[<name>] Output data set name
<mask1> Atom mask selecting atom(s) to calculate distance between.
<mask2> If specified, second atom mask selection atom(s) to calculate distance from <mask1>.
point <x><y><z> If specified instead of second mask, calculate distance between and specified XYZ coordinates.
reference | ref | refindex <#> If specified, calculate distance between <mask1> in each input frame and <mask2> in the specified reference.
[out <filename>] Output filename.
[geom] Use geometric center of atoms in <mask1>/<mask2>; default is to use center of mass.
[noimage] Do not image distances across periodic boundaries.
[type noe] Mark distance as ’noe’ for use with statistics analysis.
[bound <lower> bound <upper>] Lower and upper bounds for NOE (in Angstroms); must specify both.
[rexp <expected>] Expected value for NOE (in Angstroms); if not given ’(<lower> + <upper>)’ / 2.0 is used.
[noe_strong] Set lower and upper bounds to 1.8 and 2.9 Å respectively.
[noe_medium] Set lower and upper bounds to 2.9 and 3.5 Å respectively.
[noe_weak] Set lower and upper bounds to 3.5 and 5.0 Å respectively.

Calculate distance between the center of mass of atoms in <mask1> to atoms in <mask2>, between atoms in <mask1> from each input frame and atoms in <mask2> in specified reference, or atoms in and the specied point. If geom is specied use the geometric center instead. For periodic systems imaging is turned on by default; the noimage keyword disables imaging.

A distance can be labeled using ’type noe’ for further analysis as an NOE using the statistics analysis command.