NAME

       gmx-filter - Frequency filter trajectories, useful for making smooth movies

SYNOPSIS

          gmx filter [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                     [-ol [<.xtc/.trr/...>]] [-oh [<.xtc/.trr/...>]]
                     [-b <time>] [-e <time>] [-dt <time>] [-[no]w] [-nf <int>]
                     [-[no]all] [-[no]nojump] [-[no]fit]

DESCRIPTION

       gmx  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 that has been fitted on the coordinates in the structure
       file.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -ol [<.xtc/.trr/...>] (lowpass.xtc) (Optional)
              Trajectory: xtc trr gro g96 pdb tng

       -oh [<.xtc/.trr/...>] (highpass.xtc) (Optional)
              Trajectory: xtc trr gro g96 pdb tng

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -[no]w (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 (no)
              Write all low-pass filtered frames

       -[no]nojump (yes)
              Remove jumps of atoms across the box

       -[no]fit (no)
              Fit all frames to a reference structure

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2024, GROMACS development team