g_filter (1) - Linux Manuals

g_filter: frequency filters trajectories, useful for making smooth movies

NAME

g_filter - frequency filters trajectories, useful for making smooth movies

VERSION 4.0.1

SYNOPSIS

g_filter -f traj.xtc -s topol.tpr -n index.ndx -ol lowpass.xtc -oh highpass.xtc -[no]h -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 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 which 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

-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