g_rotmat(1) [debian man page]
g_rotmat(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_rotmat(1) NAME
g_rotmat - plots the rotation matrix for fitting to a reference structure VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_rotmat -f traj.xtc -s topol.tpr -n index.ndx -o rotmat.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -ref enum -skip int -[no]fitxy -[no]mw DESCRIPTION
g_rotmat plots the rotation matrix required for least squares fitting a conformation onto the reference conformation provided with -s. Translation is removed before fitting. The output are the three vectors that give the new directions of the x, y and z directions of the reference conformation, for example: (zx,zy,zz) is the orientation of the reference z-axis in the trajectory frame. This tool is useful for, for instance, determining the orientation of a molecule at an interface, possibly on a trajectory produced with trjconv -fit rotxy+transxy to remove the rotation in the x-y plane. Option -ref determines a reference structure for fitting, instead of using the structure from -s. The structure with the lowest sum of RMSD's to all other structures is used. Since the computational cost of this procedure grows with the square of the number of frames, the -skip option can be useful. A full fit or only a fit in the x-y plane can be performed. Option -fitxy fits in the x-y plane before determining the rotation matrix. 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 rotmat.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 -ref enum none Determine the optimal reference structure: none, xyz or xy -skip int 1 Use every nr-th frame for -ref -[no]fitxyno Fit the x/y rotation before determining the rotation -[no]mwyes Use mass weighted fitting SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_rotmat(1)
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trjorder(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c trjorder(1) NAME
trjorder - orders molecules according to their distance to a group VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
trjorder -f traj.xtc -s topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h -[no]version -nice int -b time -e time -dt time -xvg enum -na int -da int -[no]com -r real -[no]z DESCRIPTION
trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected mole- cules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. The center of mass of the molecules can be used instead of a reference atom by setting -da to 0. All atoms in the trajectory are written to the output trajectory. trjorder can be useful for e.g. analyzing the n waters closest to a protein. In that case the reference group would be the protein and the group of molecules would consist of all the water atoms. When an index group of the first n waters is made, the ordered trajectory can be used with any Gromacs program to analyze the n closest waters. If the output file is a .pdb file, the distance to the reference target will be stored in the B-factor field in order to color with e.g. Rasmol. With option -nshell the number of molecules within a shell of radius -r around the reference group are printed. 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 ordered.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb -nshell nshell.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) -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -na int 3 Number of atoms in a molecule -da int 1 Atom used for the distance calculation, 0 is COM -[no]comno Use the distance to the center of mass of the reference group -r real 0 Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein -[no]zno Order molecules on z-coordinate SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 trjorder(1)