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Difference between revisions from 2011/03/21 11:45 and 2010/03/18 15:21.

This script is used to analyse geometrical properties in MD trajectories. One measured variable can be specified at commandline, multiple variables can be defined in an input file.

It works not only with atoms, but also with groups of atoms. In the groups, their center of mass is used as the coordinate unless specified otherwise.

!!Measured properties:
* Distance between atoms or groups
* Angle
* Torsion angle
* Closest distance between groups
* Point to plane distance

!!Commandline options
{{measure [options] trajectory_file}}

* '''-i, ^-^-input ''filename'' ''' - name of the input file
* '''-e, ^-^-expression ''string'' ''' - expression to calculate (instead of using input file)
* '''-g, ^-^-reference-geometry ''filename'' ''' - geometry file containing the same system, needed only when the trajectory does not contain all information needed for the analysis (such as elements, atom types, residue names...)
*'''-q, ^-^-quiet''' - Do not print the header, just the numbers
* '''-f, ^-^-format ''string'' ''' - Format of the trajectory file:
** '''xyz''' - The XYZ format
** '''xyz_notitle_noelement''' - Coordinates only, each record contains: first line - number of atoms, following lines: coordinates of the atoms (3 numbers only, separated by whitespace)

!! Input file, expressions
Input file is a text file that can contain multiple expressions to be measured, one per line. Blank lines and lines starting with # are ignored.

Basic expressions have format:
{{expression_type(selection; selection; ...)}}
or they can be named:
{{name = expression_type(selection; selection; ...)}}

The expression types are:
* Distance between atoms or groups: {{distance(selection1; selection2)}}
* Torsion angle {{torsion(selection1; selection2; selection3; selection3)}}
* Closest distance between groups {{closest_distance(selection1; selection2)}}
* Torsion angle {{torsion(selection1; selection2; selection3; selection4)}}
* Closest distance between groups {{closest_distance(selection1; selection2)}}
* Point to plane distance - point + plane defined by three points: {{point_plane(selection1; selection2; selection3; selection4)}}