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g_helixorient(1) [debian man page]

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

NAME
g_helixorient - calculates local pitch/bending/rotation/orientation inside helices VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_helixorient -s topol.tpr -f traj.xtc -n index.ndx -oaxis helixaxis.dat -ocenter center.dat -orise rise.xvg -oradius radius.xvg -otwist twist.xvg -obending bending.xvg -otilt tilt.xvg -orot rotation.xvg -[no]h -[no]version -nice int -b time -e time -dt time -xvg enum -[no]sidechain -[no]incremental DESCRIPTION
g_helixorient calculates the coordinates and direction of the average axis inside an alpha helix, and the direction/vectors of both the Calpha and (optionally) a sidechain atom relative to the axis. As input, you need to specify an index group with Calpha atoms corresponding to an alpha-helix of continuous residues. Sidechain directions require a second index group of the same size, containing the heavy atom in each residue that should represent the sidechain. Note that this program does not do any fitting of structures. We need four Calpha coordinates to define the local direction of the helix axis. The tilt/rotation is calculated from Euler rotations, where we define the helix axis as the local x-axis, the residues/Calpha vector as y, and the z-axis from their cross product. We use the Euler Y-Z-X rotation, meaning we first tilt the helix axis (1) around and (2) orthogonal to the residues vector, and finally apply the (3) rotation around it. For debugging or other purposes, we also write out the actual Euler rotation angles as theta[1-3].xvg FILES
-s topol.tpr Input Run input file: tpr tpb tpa -f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input, Opt. Index file -oaxis helixaxis.dat Output Generic data file -ocenter center.dat Output Generic data file -orise rise.xvg Output xvgr/xmgr file -oradius radius.xvg Output xvgr/xmgr file -otwist twist.xvg Output xvgr/xmgr file -obending bending.xvg Output xvgr/xmgr file -otilt tilt.xvg Output xvgr/xmgr file -orot rotation.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) -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]sidechainno Calculate sidechain directions relative to helix axis too. -[no]incrementalno Calculate incremental rather than total rotation/tilt. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_helixorient(1)

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

NAME
g_order - computes the order parameter per atom for carbon tails VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_order -f traj.xtc -n index.ndx -nr index.ndx -s topol.tpr -o order.xvg -od deuter.xvg -ob eiwit.pdb -os sliced.xvg -Sg sg-ang.xvg -Sk sk-dist.xvg -Sgsl sg-ang-slice.xvg -Sksl sk-dist-slice.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -d enum -sl int -[no]szonly -[no]unsat -[no]permolecule -[no]radial -[no]calcdist DESCRIPTION
Compute the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. The index file should contain only the groups to be used for calculations, with each group of equivalent carbons along the relevant acyl chain in its own group. There should not be any generic groups (like System, Protein) in the index file to avoid confusing the program (this is not relevant to tetrahedral order parameters however, which only work for water anyway). The program can also give all diagonal elements of the order tensor and even calculate the deuterium order parameter Scd (default). If the option -szonly is given, only one order tensor component (specified by the -d option) is given and the order parameter per slice is cal- culated as well. If -szonly is not selected, all diagonal elements and the deuterium order parameter is given. The tetrahedrality order parameters can be determined around an atom. Both angle an distance order parameters are calculated. See P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. for more details. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input Index file -nr index.ndx Input Index file -s topol.tpr Input Run input file: tpr tpb tpa -o order.xvg Output xvgr/xmgr file -od deuter.xvg Output xvgr/xmgr file -ob eiwit.pdb Output Protein data bank file -os sliced.xvg Output xvgr/xmgr file -Sg sg-ang.xvg Output, Opt. xvgr/xmgr file -Sk sk-dist.xvg Output, Opt. xvgr/xmgr file -Sgsl sg-ang-slice.xvg Output, Opt. xvgr/xmgr file -Sksl sk-dist-slice.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 -d enum z Direction of the normal on the membrane: z, x or y -sl int 1 Calculate order parameter as function of box length, dividing the box in nr slices. -[no]szonlyno Only give Sz element of order tensor. (axis can be specified with -d) -[no]unsatno Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. -[no]permoleculeno Compute per-molecule Scd order parameters -[no]radialno Compute a radial membrane normal -[no]calcdistno Compute distance from a reference (currently defined only for radial and permolecule) SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_order(1)

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