gmx gangle
	Main Table of Contents	VERSION 5.0.5

Synopsis

gmx gangle [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
           [-oav [<.xvg>]] [-oall [<.xvg>]] [-oh [<.xvg>]] [-b ]
           [-e ] [-dt ] [-tu ] [-xvg ] [-[no]rmpbc]
           [-[no]pbc] [-sf ] [-selrpos ] [-g1 ]
           [-g2 ] [-binw ] [-group1 ]
           [-group2 ]

Description

The type of the angle is specified with -g1 and -g2. If -g1 is angle or dihedral, -g2 should not be specified. In this case, -group1 should specify one or more selections, and each should contain triplets or quartets of positions that define the angles to be calculated.

If -g1 is vector or plane, -group1 should specify selections that contain either pairs (vector) or triplets (plane) of positions. For vectors, the positions set the endpoints of the vector, and for planes, the three positions are used to calculate the normal of the plane. In both cases, -g2 specifies the other vector to use (see below).

With -g2 vector or -g2 plane, -group2 should specify another set of vectors. -group1 and -group2 should specify the same number of selections. It is also allowed to only have a single selection for one of the options, in which case the same selection is used with each selection in the other group. Similarly, for each selection in -group1, the corresponding selection in -group2 should specify the same number of vectors or a single vector. In the latter case, the angle is calculated between that single vector and each vector from the other selection.

With -g2 sphnorm, each selection in -group2 should specify a single position that is the center of the sphere. The second vector is calculated as the vector from the center to the midpoint of the positions specified by -group1.

With -g2 z, -group2 is not necessary, and angles between the first vectors and the positive Z axis are calculated.

With -g2 t0, -group2 is not necessary, and angles are calculated from the vectors as they are in the first frame.

There are three options for output: -oav writes an xvg file with the time and the average angle for each frame. -oall writes all the individual angles. -oh writes a histogram of the angles. The bin width can be set with -binw. For -oav and -oh, separate average/histogram is computed for each selection in -group1.

Options

-f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)

Input trajectory or single configuration: xtc trr cpt trj gro g96 pdb tng

-s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)

Input structure: tpr tpb tpa gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Input, Optional)

Extra index groups

-oav [<.xvg>] (angaver.xvg) (Output, Optional)

Average angles as a function of time

-oall [<.xvg>] (angles.xvg) (Output, Optional)

All angles as a function of time

-oh [<.xvg>] (anghist.xvg) (Output, Optional)

Histogram of the angles

-b <time> (0)

First frame (ps) to read from trajectory

-e <time> (0)

Last frame (ps) to read from trajectory

-dt <time> (0)

Only use frame if t MOD dt == first time (ps)

-tu <enum> (ps)

Unit for time values: fs, ps, ns, us, ms, s

-xvg <enum> (xmgrace)

Plot formatting: none, xmgrace, xmgr

-[no]rmpbc (yes)

Make molecules whole for each frame

-[no]pbc (yes)

Use periodic boundary conditions for distance calculation

-sf <file>

Provide selections from files

-selrpos <enum> (atom)

Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

-g1 <enum> (angle)

Type of analysis/first vector group: angle, dihedral, vector, plane

-g2 <enum> (none)

Type of second vector group: none, vector, plane, t0, z, sphnorm

-binw <real> (1)

Binwidth for -oh in degrees

-group1 <selection>

First analysis/vector selection

-group2 <selection>

Second analysis/vector selection