gmx hydorder¶
Synopsis¶
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>]
Description¶
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