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.TH "GMX-GANGLE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
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.SH NAME
gmx-gangle \- Calculate angles
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.SH SYNOPSIS
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
gmx gangle [\fB\-f\fP \fI[<.xtc/.trr/...>]\fP] [\fB\-s\fP \fI[<.tpr/.gro/...>]\fP] [\fB\-n\fP \fI[<.ndx>]\fP]
           [\fB\-oav\fP \fI[<.xvg>]\fP] [\fB\-oall\fP \fI[<.xvg>]\fP] [\fB\-oh\fP \fI[<.xvg>]\fP]
           [\fB\-b\fP \fI<time>\fP] [\fB\-e\fP \fI<time>\fP] [\fB\-dt\fP \fI<time>\fP] [\fB\-tu\fP \fI<enum>\fP]
           [\fB\-fgroup\fP \fI<selection>\fP] [\fB\-xvg\fP \fI<enum>\fP] [\fB\-[no]rmpbc\fP]
           [\fB\-[no]pbc\fP] [\fB\-sf\fP \fI<file>\fP] [\fB\-selrpos\fP \fI<enum>\fP]
           [\fB\-seltype\fP \fI<enum>\fP] [\fB\-g1\fP \fI<enum>\fP] [\fB\-g2\fP \fI<enum>\fP] [\fB\-binw\fP \fI<real>\fP]
           [\fB\-group1\fP \fI<selection>\fP] [\fB\-group2\fP \fI<selection>\fP]
.ft P
.fi
.UNINDENT
.UNINDENT
.SH DESCRIPTION
.sp
\fBgmx gangle\fP computes different types of angles between vectors.
It supports both vectors defined by two positions and normals of
planes defined by three positions.
The z axis or the local normal of a sphere can also be used as
one of the vectors.
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There are also convenience options ‘angle’ and ‘dihedral’ for
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calculating bond angles and dihedrals defined by three/four
positions.
.sp
The type of the angle is specified with \fB\-g1\fP and \fB\-g2\fP\&.
If \fB\-g1\fP is \fBangle\fP or \fBdihedral\fP, \fB\-g2\fP
should not be specified.
In this case, \fB\-group1\fP should specify one or more selections,
and each should contain triplets or quartets of positions that define
the angles to be calculated.
.sp
If \fB\-g1\fP is \fBvector\fP or \fBplane\fP, \fB\-group1\fP
should specify selections that contain either pairs (\fBvector\fP)
or triplets (\fBplane\fP) 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,
\fB\-g2\fP specifies the other vector to use (see below).
.sp
With \fB\-g2 vector\fP or \fB\-g2 plane\fP, \fB\-group2\fP should
specify another set of vectors. \fB\-group1\fP and \fB\-group2\fP
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 \fB\-group1\fP, the corresponding
selection in \fB\-group2\fP 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.
.sp
With \fB\-g2 sphnorm\fP, each selection in \fB\-group2\fP 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 \fB\-group1\fP\&.
.sp
With \fB\-g2 z\fP, \fB\-group2\fP is not necessary, and angles
between the first vectors and the positive Z axis are calculated.
.sp
With \fB\-g2 t0\fP, \fB\-group2\fP is not necessary, and angles
are calculated from the vectors as they are in the first frame.
.sp
There are three options for output:
\fB\-oav\fP writes an xvg file with the time and the average angle
for each frame.
\fB\-oall\fP writes all the individual angles.
\fB\-oh\fP writes a histogram of the angles. The bin width can be
set with \fB\-binw\fP\&.
For \fB\-oav\fP and \fB\-oh\fP, separate average/histogram is
computed for each selection in \fB\-group1\fP\&.
.SH OPTIONS
.sp
Options to specify input files:
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.TP
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.B \fB\-f\fP [<.xtc/.trr/…>] (traj.xtc) (Optional)
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Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
.TP
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.B \fB\-s\fP [<.tpr/.gro/…>] (topol.tpr) (Optional)
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Input structure: tpr gro g96 pdb brk ent
.TP
.B \fB\-n\fP [<.ndx>] (index.ndx) (Optional)
Extra index groups
.UNINDENT
.sp
Options to specify output files:
.INDENT 0.0
.TP
.B \fB\-oav\fP [<.xvg>] (angaver.xvg) (Optional)
Average angles as a function of time
.TP
.B \fB\-oall\fP [<.xvg>] (angles.xvg) (Optional)
All angles as a function of time
.TP
.B \fB\-oh\fP [<.xvg>] (anghist.xvg) (Optional)
Histogram of the angles
.UNINDENT
.sp
Other options:
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.TP
.B \fB\-b\fP <time> (0)
First frame (ps) to read from trajectory
.TP
.B \fB\-e\fP <time> (0)
Last frame (ps) to read from trajectory
.TP
.B \fB\-dt\fP <time> (0)
Only use frame if t MOD dt == first time (ps)
.TP
.B \fB\-tu\fP <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
.TP
.B \fB\-fgroup\fP <selection>
Atoms stored in the trajectory file (if not set, assume first N atoms)
.TP
.B \fB\-xvg\fP <enum> (xmgrace)
Plot formatting: none, xmgrace, xmgr
.TP
.B \fB\-[no]rmpbc\fP  (yes)
Make molecules whole for each frame
.TP
.B \fB\-[no]pbc\fP  (yes)
Use periodic boundary conditions for distance calculation
.TP
.B \fB\-sf\fP <file>
Provide selections from files
.TP
.B \fB\-selrpos\fP <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
.TP
.B \fB\-seltype\fP <enum> (atom)
Default selection output 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
.TP
.B \fB\-g1\fP <enum> (angle)
Type of analysis/first vector group: angle, dihedral, vector, plane
.TP
.B \fB\-g2\fP <enum> (none)
Type of second vector group: none, vector, plane, t0, z, sphnorm
.TP
.B \fB\-binw\fP <real> (1)
Binwidth for \-oh in degrees
.TP
.B \fB\-group1\fP <selection>
First analysis/vector selection
.TP
.B \fB\-group2\fP <selection>
Second analysis/vector selection
.UNINDENT
.SH SEE ALSO
.sp
\fBgmx(1)\fP
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
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2018, GROMACS development team
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