g_sgangle(1) [debian man page]
g_sgangle(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_sgangle(1) NAME
g_sgangle - computes the angle and distance between two groups VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_sgangle -f traj.xtc -n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]one -[no]z DESCRIPTION
Compute the angle and distance between two groups. The groups are defined by a number of atoms given in an index file and may be two or three atoms in size. If -one is set, only one group should be specified in the index file and the angle between this group at time 0 and t will be computed. The angles calculated depend on the order in which the atoms are given. Giving, for instance, 5 6 will rotate the vec- tor 5-6 with 180 degrees compared to giving 6 5. If three atoms are given, the normal on the plane spanned by those three atoms will be calculated, using the formula P1P2 x P1P3. The cos of the angle is calculated, using the inproduct of the two normalized vectors. Here is what some of the file options do: -oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used. -od: Distance between two groups. Distance is taken from the center of one group to the center of the other group. -od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately. -od2: For two planes this option has no meaning. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input Index file -s topol.tpr Input Run input file: tpr tpb tpa -oa sg_angle.xvg Output xvgr/xmgr file -od sg_dist.xvg Output, Opt. xvgr/xmgr file -od1 sg_dist1.xvg Output, Opt. xvgr/xmgr file -od2 sg_dist2.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 -[no]oneno Only one group compute angle between vector at time zero and time t -[no]zno Use the z-axis as reference SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_sgangle(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)