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g_densmap(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_densmap(1)

NAME
g_densmap - calculates 2D planar or axial-radial density maps VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_densmap -f traj.xtc -s topol.tpr -n index.ndx -od densmap.dat -o densmap.xpm -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -bin real -aver enum -xmin real -xmax real -n1 int -n2 int -amax real -rmax real -[no]mirror -[no]sums -unit enum -dmin real -dmax real DESCRIPTION
g_densmap computes 2D number-density maps. It can make planar and axial-radial density maps. The output .xpm file can be visualized with for instance xv and can be converted to postscript with xpm2ps. Optionally, output can be in text form to a .dat file with -od, instead of the usual .xpm file with -o. The default analysis is a 2-D number-density map for a selected group of atoms in the x-y plane. The averaging direction can be changed with the option -aver. When -xmin and/or -xmax are set only atoms that are within the limit(s) in the averaging direction are taken into account. The grid spacing is set with the option -bin. When -n1 or -n2 is non-zero, the grid size is set by this option. Box size fluctuations are properly taken into account. When options -amax and -rmax are set, an axial-radial number-density map is made. Three groups should be supplied, the centers of mass of the first two groups define the axis, the third defines the analysis group. The axial direction goes from -amax to +amax, where the center is defined as the midpoint between the centers of mass and the positive direction goes from the first to the second center of mass. The radial direction goes from 0 to rmax or from -rmax to +rmax when the -mirror option has been set. The normalization of the output is set with the -unit option. The default produces a true number density. Unit nm-2 leaves out the nor- malization for the averaging or the angular direction. Option count produces the count for each grid cell. When you do not want the scale in the output to go from zero to the maximum density, you can set the maximum with the option -dmax. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -od densmap.dat Output, Opt. Generic data file -o densmap.xpm Output X PixMap compatible matrix 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 -bin real 0.02 Grid size (nm) -aver enum z The direction to average over: z, y or x -xmin real -1 Minimum coordinate for averaging -xmax real -1 Maximum coordinate for averaging -n1 int 0 Number of grid cells in the first direction -n2 int 0 Number of grid cells in the second direction -amax real 0 Maximum axial distance from the center -rmax real 0 Maximum radial distance -[no]mirrorno Add the mirror image below the axial axis -[no]sumsno Print density sums (1D map) to stdout -unit enum nm-3 Unit for the output: nm-3, nm-2 or count -dmin real 0 Minimum density in output -dmax real 0 Maximum density in output (0 means calculate it) SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_densmap(1)

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g_bond(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					 g_bond(1)

NAME
g_bond - calculates distances between atoms VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_bond -f traj.xtc -n index.ndx -s topol.tpr -o bonds.xvg -l bonds.log -d distance.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -blen real -tol real -[no]aver -[no]averdist DESCRIPTION
g_bond makes a distribution of bond lengths. If all is well a Gaussian distribution should be made when using a harmonic potential. Bonds are read from a single group in the index file in order i1-j1 i2-j2 through in-jn. -tol gives the half-width of the distribution as a fraction of the bondlength ( -blen). That means, for a bond of 0.2 a tol of 0.1 gives a distribution from 0.18 to 0.22. Option -d plots all the distances as a function of time. This requires a structure file for the atom and residue names in the output. If however the option -averdist is given (as well or separately) the average bond length is plotted instead. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input Index file -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -o bonds.xvg Output xvgr/xmgr file -l bonds.log Output, Opt. Log file -d distance.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) -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -blen real -1 Bond length. By default length of first bond -tol real 0.1 Half width of distribution as fraction of blen -[no]averyes Average bond length distributions -[no]averdistyes Average distances (turns on -d) KNOWN PROBLEMS
- It should be possible to get bond information from the topology. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_bond(1)
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