07-07-2008
inserting a new line in a file
I'm sure you guys have answered this elsewhere but I can't seem to find where so here goes.
#!/bin/bash
n=120
a=$(sed '120q;d' energy.xvg)
while [ a != exit ];do
a=$(sed $n'q;d' energy.xvg)
echo "$a \n" > newfile
n=$(($n+100))
done
exit 0
that script should read the file energy.xvg, start at line 120, and copy every 100th line to newfile. The problem is that it only outputs to one line in the file and so every line overwrites the one before it. I want it to write to a new line each time.
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LEARN ABOUT DEBIAN
g_sgangle
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)