g_disre(1) [debian man page]
g_disre(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_disre(1) NAME
g_disre - analyzes distance restraints VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_disre -s topol.tpr -f traj.xtc -ds drsum.xvg -da draver.xvg -dn drnum.xvg -dm drmax.xvg -dr restr.xvg -l disres.log -n viol.ndx -q viol.pdb -c clust.ndx -x matrix.xpm -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -ntop int -maxdr real -nlevels int -[no]third DESCRIPTION
g_disre computes violations of distance restraints. If necessary, all protons can be added to a protein molecule using the g_protonate program. The program always computes the instantaneous violations rather than time-averaged, because this analysis is done from a trajectory file afterwards it does not make sense to use time averaging. However, the time averaged values per restraint are given in the log file. An index file may be used to select specific restraints for printing. When the optional -q flag is given a .pdb file coloured by the amount of average violations. When the -c option is given, an index file will be read containing the frames in your trajectory corresponding to the clusters (defined in another manner) that you want to analyze. For these clusters the program will compute average violations using the third power averaging algorithm and print them in the log file. FILES
-s topol.tpr Input Run input file: tpr tpb tpa -f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -ds drsum.xvg Output xvgr/xmgr file -da draver.xvg Output xvgr/xmgr file -dn drnum.xvg Output xvgr/xmgr file -dm drmax.xvg Output xvgr/xmgr file -dr restr.xvg Output xvgr/xmgr file -l disres.log Output Log file -n viol.ndx Input, Opt. Index file -q viol.pdb Output, Opt. Protein data bank file -c clust.ndx Input, Opt. Index file -x matrix.xpm Output, Opt. 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 -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -ntop int 0 Number of large violations that are stored in the log file every step -maxdr real 0 Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data. -nlevels int 20 Number of levels in the matrix output -[no]thirdyes Use inverse third power averaging or linear for matrix output SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_disre(1)
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g_bundle(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_bundle(1) NAME
g_bundle - analyzes bundles of axes, e.g. helices VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_bundle -f traj.xtc -s topol.tpr -n index.ndx -ol bun_len.xvg -od bun_dist.xvg -oz bun_z.xvg -ot bun_tilt.xvg -otr bun_tiltr.xvg -otl bun_tiltl.xvg -ok bun_kink.xvg -okr bun_kinkr.xvg -okl bun_kinkl.xvg -oa axes.pdb -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -xvg enum -na int -[no]z DESCRIPTION
g_bundle analyzes bundles of axes. The axes can be for instance helix axes. The program reads two index groups and divides both of them in -na parts. The centers of mass of these parts define the tops and bottoms of the axes. Several quantities are written to file: the axis length, the distance and the z-shift of the axis mid-points with respect to the average center of all axes, the total tilt, the radial tilt and the lateral tilt with respect to the average axis. With options -ok, -okr and -okl the total, radial and lateral kinks of the axes are plotted. An extra index group of kink atoms is required, which is also divided into -na parts. The kink angle is defined as the angle between the kink-top and the bottom-kink vectors. With option -oa the top, mid (or kink when -ok is set) and bottom points of each axis are written to a .pdb file each frame. The residue numbers correspond to the axis numbers. When viewing this file with Rasmol, use the command line option -nmrpdb, and type set axis true to display the reference axis. 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 -ol bun_len.xvg Output xvgr/xmgr file -od bun_dist.xvg Output xvgr/xmgr file -oz bun_z.xvg Output xvgr/xmgr file -ot bun_tilt.xvg Output xvgr/xmgr file -otr bun_tiltr.xvg Output xvgr/xmgr file -otl bun_tiltl.xvg Output xvgr/xmgr file -ok bun_kink.xvg Output, Opt. xvgr/xmgr file -okr bun_kinkr.xvg Output, Opt. xvgr/xmgr file -okl bun_kinkl.xvg Output, Opt. xvgr/xmgr file -oa axes.pdb Output, Opt. Protein data bank 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) -tu enum ps Time unit: fs, ps, ns, us, ms or s -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -na int 0 Number of axes -[no]zno Use the z-axis as reference instead of the average axis SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_bundle(1)