Main Table of Contents

Fri 5 Jul 2013


g_filter performs frequency filtering on a trajectory. The filter shape is cos(π 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 properties 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.


-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]h bool no Print help info and quit
-[no]version bool no 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]w bool no 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]all bool no Write all low-pass filtered frames
-[no]nojump bool yes Remove jumps of atoms across the box
-[no]fit bool no Fit all frames to a reference structure