g_hydorder

Main Table of Contents

VERSION 4.6.4
Wed 13 Nov 2013


Description

g_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.
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

optionfilenametypedescription
-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

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]version bool no 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]w bool no 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


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