g_hydorder(1) computes tetrahedrality parameters around a given atom


g_hydorder -f traj.xtc -n index.ndx -s topol.tpr -o intf.xpm -or raw.out -Spect intfspect.out -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -d enum -bw real -sgang1 real -sgang2 real -tblock int -nlevel int


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)


-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 


 Print help info and quit

 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)

 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