g_filter(1) [debian man page]
g_filter(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_filter(1) NAME
g_filter - frequency filters trajectories, useful for making smooth movies VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_filter -f traj.xtc -s topol.tpr -n index.ndx -ol lowpass.xtc -oh highpass.xtc -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -nf int -[no]all -[no]nojump -[no]fit DESCRIPTION
g_filter performs frequency filtering on a trajectory. The filter shape is cos(pi t/A) + 1 from -A to +A, where A is given by the option -nf times the time step in the input trajectory. This filter reduces fluctuations with period A by 85%, with period 2*A by 50% and with period 3*A by 17% for low-pass filtering. Both a low-pass and high-pass filtered trajectory can be written. Option -ol writes a low-pass filtered trajectory. A frame is written every -nf input frames. This ratio of filter length and output interval ensures a good suppression of aliasing of high-frequency motion, which is useful for making smooth movies. Also averages of prop- erties which are linear in the coordinates are preserved, since all input frames are weighted equally in the output. When all frames are needed, use the -all option. Option -oh writes a high-pass filtered trajectory. The high-pass filtered coordinates are added to the coordinates from the structure file. When using high-pass filtering use -fit or make sure you use a trajectory that has been fitted on the coordinates in the structure file. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -ol lowpass.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb -oh highpass.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb 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 -nf int 10 Sets the filter length as well as the output interval for low-pass filtering -[no]allno Write all low-pass filtered frames -[no]nojumpyes Remove jumps of atoms across the box -[no]fitno Fit all frames to a reference structure SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_filter(1)
Check Out this Related Man Page
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)