This is the command gmx-hydorder that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-hydorder - Compute tetrahedrality parameters around a given atom
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)
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 (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
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