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/>.