gmx-hydorder1
Compute tetrahedrality parameters around a given atom
Usage
gmx hydorder [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s [<.tpr>]]
[-o [<.xpm> [...]]] [-or [<.out> [...]]]
[-Spect [<.out> [...]]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-d <enum>] [-bw <real>]
[-sgang1 <real>] [-sgang2 <real>] [-tblock <int>]
[-nlevel <int>]
Overview
gmx 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.
gmx hydorder calculates the order parameter 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).
Options
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
|
Trajectory: xtc trr cpt gro g96 pdb tng |
|---|---|
-n [<.ndx>] (index.ndx)
|
Index file |
-s [<.tpr>] (topol.tpr)
|
Portable xdr run input file |
Options to specify output files:
-o [<.xpm> [...]] (intf.xpm)
|
X PixMap compatible matrix file |
|---|---|
-or [<.out> [...]] (raw.out) (Optional)
|
Generic output 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 |
-d <enum> (z)
|
Direction of the normal on the membrane: z, x, 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 |
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.