mk_angndx(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c mk_angndx(1)NAME
mk_angndx - generates index files for g_angle
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
mk_angndx -s topol.tpr -n angle.ndx -[no]h -[no]version -nice int -type enum -[no]hyd -hq real
DESCRIPTION
mk_angndx makes an index file for calculation of angle distributions etc. It uses a run input file ( .tpx) for the definitions of the
angles, dihedrals etc.
FILES -s topol.tpr Input
Run input file: tpr tpb tpa
-n angle.ndx Output
Index file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-type enum angle
Type of angle: angle, dihedral, improper or ryckaert-bellemans
-[no]hydyes
Include angles with atoms with mass 1.5
-hq real -1
Ignore angles with atoms with mass 1.5 and |q| hq
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 mk_angndx(1)
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g_sgangle(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_sgangle(1)NAME
g_sgangle - computes the angle and distance between two groups
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_sgangle -f traj.xtc -n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg -[no]h -[no]version
-nice int -b time -e time -dt time -[no]w -xvg enum -[no]one -[no]z
DESCRIPTION
Compute the angle and distance between two groups. The groups are defined by a number of atoms given in an index file and may be two or
three atoms in size. If -one is set, only one group should be specified in the index file and the angle between this group at time 0 and
t will be computed. The angles calculated depend on the order in which the atoms are given. Giving, for instance, 5 6 will rotate the vec-
tor 5-6 with 180 degrees compared to giving 6 5.
If three atoms are given, the normal on the plane spanned by those three atoms will be calculated, using the formula P1P2 x P1P3. The cos
of the angle is calculated, using the inproduct of the two normalized vectors.
Here is what some of the file options do:
-oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those
three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.
-od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.
-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.
-od2: For two planes this option has no meaning.
FILES -f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input
Index file
-s topol.tpr Input
Run input file: tpr tpb tpa
-oa sg_angle.xvg Output
xvgr/xmgr file
-od sg_dist.xvg Output, Opt.
xvgr/xmgr file
-od1 sg_dist1.xvg Output, Opt.
xvgr/xmgr file
-od2 sg_dist2.xvg Output, Opt.
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 19
Set the nicelevel
-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 when t MOD dt = first time (ps)
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-[no]oneno
Only one group compute angle between vector at time zero and time t
-[no]zno
Use the z-axis as reference
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_sgangle(1)