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g_densorderMain Table of Contents |
VERSION 4.6.5
Mon 2 Dec 2013
| VERSION 4.6.5 |
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
| option | filename | type | description |
|---|---|---|---|
| -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 |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -[no]version | bool | no | 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]w | bool | no | View output .xvg, .xpm, .eps and .pdb files |
| -[no]1d | bool | 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 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 |