g_bundle(1) [debian man page]
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)
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g_rmsf(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_rmsf(1) NAME
g_rmsf - calculates atomic fluctuations VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_rmsf -f traj.xtc -s topol.tpr -n index.ndx -q eiwit.pdb -oq bfac.pdb -ox xaver.pdb -o rmsf.xvg -od rmsdev.xvg -oc correl.xvg -dir rmsf.log -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]res -[no]aniso -[no]fit DESCRIPTION
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory (supplied with -f) after (optionally) fitting to a reference frame (supplied with -s). With option -oq the RMSF values are converted to B-factor values, which are written to a .pdb file with the coordinates, of the structure file, or of a .pdb file when -q is specified. Option -ox writes the B-factors to a file with the average coordinates. With the option -od the root mean square deviation with respect to the reference structure is calculated. With the option -aniso, g_rmsf will compute anisotropic temperature factors and then it will also output average coordinates and a .pdb file with ANISOU records (corresonding to the -oq or -ox option). Please note that the U values are orientation-dependent, so before com- parison with experimental data you should verify that you fit to the experimental coordinates. When a .pdb input file is passed to the program and the -aniso flag is set a correlation plot of the Uij will be created, if any aniso- tropic temperature factors are present in the .pdb file. With option -dir the average MSF (3x3) matrix is diagonalized. This shows the directions in which the atoms fluctuate the most and the least. 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 -q eiwit.pdb Input, Opt. Protein data bank file -oq bfac.pdb Output, Opt. Protein data bank file -ox xaver.pdb Output, Opt. Protein data bank file -o rmsf.xvg Output xvgr/xmgr file -od rmsdev.xvg Output, Opt. xvgr/xmgr file -oc correl.xvg Output, Opt. xvgr/xmgr file -dir rmsf.log Output, Opt. Log 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 -[no]resno Calculate averages for each residue -[no]anisono Compute anisotropic termperature factors -[no]fityes Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_rmsf(1)