04-12-2011
Doesn't get it outside, k=$(( $k + 3 )), so that is not an issue.
I like 11 as the right answer, so $ is necessary? Mult takes precedence over + ? Or left to right, it should be 15. Ugly! I always use paren. no priority applicable.
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LEARN ABOUT DEBIAN
g_densorder
g_densorder(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_densorder(1)
NAME
g_densorder - calculate surface fluctuations
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_densorder -s topol.tpr -f traj.xtc -n index.ndx -o Density4D.dat -or hello.out -og interface.xpm -Spect intfspect.out -[no]h -[no]version
-nice int -b time -e time -dt time -[no]w -[no]1d -bw real -bwn real -order int -axis string -method enum -d1 real -d2 real -tblock int
-nlevel int
DESCRIPTION
A small program to reduce a two-phase density distribution along an axis, computed over a MD trajectory to 2D surfaces fluctuating in time,
by a fit to a functional profile for interfacial densities A time-averaged spatial representation of the interfaces can be output with the
option -tavg
FILES
-s topol.tpr Input
Run input file: tpr tpb tpa
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input
Index file
-o Density4D.dat Output, Opt.
Generic data file
-or hello.out Output, Opt., Mult.
Generic output file
-og interface.xpm Output, Opt., Mult.
X PixMap compatible matrix file
-Spect intfspect.out Output, Opt., Mult.
Generic output file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
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
-[no]1dno
Pseudo-1d interface geometry
-bw real 0.2
Binwidth of density distribution tangential to interface
-bwn real 0.05
Binwidth of density distribution normal to interface
-order int 0
Order of Gaussian filter, order 0 equates to NO filtering
-axis string Z
Axis Direction - X, Y or Z
-method enum bisect
Interface location method: bisect or functional
-d1 real 0
Bulk density phase 1 (at small z)
-d2 real 1000
Bulk density phase 2 (at large z)
-tblock int 100
Number of frames in one time-block average
-nlevel int 100
Number of Height levels in 2D - XPixMaps
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_densorder(1)