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_sorient(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_sorient(1) NAME
g_sorient - analyzes solvent orientation around solutes VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -rc scount.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]com -[no]v23 -rmin real -rmax real -cbin real -rbin real -[no]pbc DESCRIPTION
g_sorient analyzes solvent orientation around solutes. It calculates two angles between the vector from one or more reference positions to the first atom of each solvent molecule: theta1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3. theta2: the angle with the normal of the solvent plane, defined by the same three atoms, or, when the option -v23 is set, the angle with the vector between atoms 2 and 3. The reference can be a set of atoms or the center of mass of a set of atoms. The group of solvent atoms should consist of 3 atoms per sol- vent molecule. Only solvent molecules between -rmin and -rmax are considered for -o and -no each frame. -o: distribtion of cos(theta1) for rmin=r=rmax. -no: distribution of cos(theta2) for rmin=r=rmax. -ro: cos(theta1) and 3cos2(theta2)-1 as a function of the distance. -co: the sum over all solvent molecules within distance r of cos(theta1) and 3cos2(theta2)-1 as a function of r. -rc: the distribution of the solvent molecules as a function of r 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 -o sori.xvg Output xvgr/xmgr file -no snor.xvg Output xvgr/xmgr file -ro sord.xvg Output xvgr/xmgr file -co scum.xvg Output xvgr/xmgr file -rc scount.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 -[no]comno Use the center of mass as the reference postion -[no]v23no Use the vector between atoms 2 and 3 -rmin real 0 Minimum distance (nm) -rmax real 0.5 Maximum distance (nm) -cbin real 0.02 Binwidth for the cosine -rbin real 0.02 Binwidth for r (nm) -[no]pbcno Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_sorient(1)