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)
Check Out this Related Man Page
g_h2order(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_h2order(1) NAME
g_h2order - computes the orientation of water molecules VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_h2order -f traj.xtc -n index.ndx -nm index.ndx -s topol.tpr -o order.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -d string -sl int DESCRIPTION
g_h2order computes the orientation of water molecules with respect to the normal of the box. The program determines the average cosine of the angle between the dipole moment of water and an axis of the box. The box is divided in slices and the average orientation per slice is printed. Each water molecule is assigned to a slice, per time frame, based on the position of the oxygen. When -nm is used, the angle between the water dipole and the axis from the center of mass to the oxygen is calculated instead of the angle between the dipole and a box axis. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input Index file -nm index.ndx Input, Opt. Index file -s topol.tpr Input Run input file: tpr tpb tpa -o order.xvg Output 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) -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -d string Z Take the normal on the membrane in direction X, Y or Z. -sl int 0 Calculate order parameter as function of boxlength, dividing the box in nr slices. KNOWN PROBLEMS
- The program assigns whole water molecules to a slice, based on the first atom of three in the index file group. It assumes an order O,H,H. Name is not important, but the order is. If this demand is not met, assigning molecules to slices is different. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_h2order(1)