g_h2order(1) [debian 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)
Check Out this Related Man Page
g_density(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_density(1) NAME
g_density - calculates the density of the system VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_density -f traj.xtc -n index.ndx -s topol.tpr -ei electrons.dat -o density.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -d string -sl int -dens enum -ng int -[no]symm -[no]center DESCRIPTION
Compute partial densities across the box, using an index file. For the total density of NPT simulations, use g_energy instead. Densities are in kg/m3, and number densities or electron densities can also be calculated. For electron densities, a file describing the number of electrons for each type of atom should be provided using -ei. It should look like: 2 atomname = nrelectrons atomname = nrelectrons The first line contains the number of lines to read from the file. There should be one line for each unique atom name in your system. The number of electrons for each atom is modified by its atomic partial charge. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input, Opt. Index file -s topol.tpr Input Run input file: tpr tpb tpa -ei electrons.dat Input, Opt. Generic data file -o density.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 50 Divide the box in nr slices. -dens enum mass Density: mass, number, charge or electron -ng int 1 Number of groups to compute densities of -[no]symmno Symmetrize the density along the axis, with respect to the center. Useful for bilayers. -[no]centerno Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass will be at bX/2, bY/2, 0. KNOWN PROBLEMS
- When calculating electron densities, atomnames are used instead of types. This is bad. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_density(1)