g_hydorder(1) - Linux man page

Name

g_hydorder VERSION 4.5.4-dev-20110404-bc5695c

Synopsis

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 -sgang1real -sgang2 real -tblock int -nlevel int

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)

Files

-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

Other Options

-[no]hno Print help info and quit

-[no]versionno 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)

-[no]wno 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