g_hydorder(1) [debian man page]
g_hydorder(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_hydorder(1) NAME
g_hydorder - computes tetrahedrality parameters around a given atom 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 -sgang1 real -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 parame- ters -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 -nlevel int 100 Number of Height levels in 2D - XPixMaps SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_hydorder(1)
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trjorder(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c trjorder(1) NAME
trjorder - orders molecules according to their distance to a group VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
trjorder -f traj.xtc -s topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h -[no]version -nice int -b time -e time -dt time -xvg enum -na int -da int -[no]com -r real -[no]z DESCRIPTION
trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected mole- cules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. The center of mass of the molecules can be used instead of a reference atom by setting -da to 0. All atoms in the trajectory are written to the output trajectory. trjorder can be useful for e.g. analyzing the n waters closest to a protein. In that case the reference group would be the protein and the group of molecules would consist of all the water atoms. When an index group of the first n waters is made, the ordered trajectory can be used with any Gromacs program to analyze the n closest waters. If the output file is a .pdb file, the distance to the reference target will be stored in the B-factor field in order to color with e.g. Rasmol. With option -nshell the number of molecules within a shell of radius -r around the reference group are printed. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -o ordered.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb -nshell nshell.xvg Output, Opt. xvgr/xmgr 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) -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -na int 3 Number of atoms in a molecule -da int 1 Atom used for the distance calculation, 0 is COM -[no]comno Use the distance to the center of mass of the reference group -r real 0 Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein -[no]zno Order molecules on z-coordinate SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 trjorder(1)