.TH g_hydorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_hydorder \- computes tetrahedrality parameters around a given atom
.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_hydorder\fP
.BI "\-f" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-s" " topol.tpr "
.BI "\-o" " intf.xpm "
.BI "\-or" " raw.out "
.BI "\-Spect" " intfspect.out "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-d" " enum "
.BI "\-bw" " real "
.BI "\-sgang1" " real "
.BI "\-sgang2" " real "
.BI "\-tblock" " int "
.BI "\-nlevel" " int "
.SH DESCRIPTION
\&The tetrahedrality order parameters can be determined
\&around an 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)
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input
 Index file 

.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-o" " intf.xpm" 
.B Output, Mult.
 X PixMap compatible matrix file 

.BI "\-or" " raw.out" 
.B Output, Opt., Mult.
 Generic output file 

.BI "\-Spect" " intfspect.out" 
.B Output, Opt., Mult.
 Generic output file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-d"  " enum" " z" 
 Direction of the normal on the membrane: \fB z\fR, \fB x\fR or \fB y\fR

.BI "\-bw"  " real" " 1     " 
 Binwidth of box mesh

.BI "\-sgang1"  " real" " 1     " 
 tetrahedral angle parameter in Phase 1 (bulk)

.BI "\-sgang2"  " real" " 1     " 
 tetrahedral angle parameter in Phase 2 (bulk)

.BI "\-tblock"  " int" " 1" 
 Number of frames in one time\-block average

.BI "\-nlevel"  " int" " 100" 
 Number of Height levels in 2D \- XPixMaps

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.