gmx-densorder man page
gmx-densorder — Calculate surface fluctuations
Synopsis
gmx densorder [
-s [<.tpr>]] [
-f [<.xtc/.trr/...>]] [
-n [<.ndx>]] [
-o [<.dat>]] [
-or [<.out> [...]]] [
-og [<.xpm> [...]]] [
-Spect [<.out> [...]]] [
-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
gmx densorder reduces 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.
Options
Options to specify input files:
- -s [<.tpr>] (topol.tpr)
Portable xdr run input file
- -f [<.xtc/.trr/…>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
- -n [<.ndx>] (index.ndx)
Index file
Options to specify output files:
- -o [<.dat>] (Density4D.dat) (Optional)
Generic data file
- -or [<.out> […]] (hello.out) (Optional)
Generic output file
- -og [<.xpm> […]] (interface.xpm) (Optional)
X PixMap compatible matrix file
- -Spect [<.out> […]] (intfspect.out) (Optional)
Generic output file
Other options:
- -b <time> (0)
Time of first frame to read from trajectory (default unit ps)
- -e <time> (0)
Time of last frame to read from trajectory (default unit ps)
- -dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
- -[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
- -[no]1d (no)
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, 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
More information about GROMACS is available at <http://www.gromacs.org/>.
Copyright
2018, GROMACS development team