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g_hydorderMain Table of Contents |
VERSION 4.6.3
Fri 5 Jul 2013
| VERSION 4.6.3 |
g_hydorder computes the tetrahedrality order parameters around a
given atom. Both angle an distance order parameters are calculated. See
P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.
for more details.
This application calculates the orderparameter in a 3d-mesh in the box, and
with 2 phases in the box gives the user the option to define a 2D interface in time
separating the faces by specifying parameters -sgang1 and -sgang2 (It is important
to select these judiciously)
| option | filename | type | description |
|---|---|---|---|
| -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 |
| -o | intf.xpm | Output, Mult. | X PixMap compatible matrix file |
| -or | raw.out | Output, Opt., Mult. | Generic output 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 | 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]w | bool | no | View output .xvg, .xpm, .eps and .pdb files |
| -d | enum | z | Direction of the normal on the membrane: z, x or y |
| -bw | real | 1 | Binwidth of box mesh |
| -sgang1 | real | 1 | tetrahedral angle parameter in Phase 1 (bulk) |
| -sgang2 | real | 1 | tetrahedral angle parameter in Phase 2 (bulk) |
| -tblock | int | 1 | Number of frames in one time-block average |
| -nlevel | int | 100 | Number of Height levels in 2D - XPixMaps |