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]
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.
-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
-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
or make sure you use a trajectory that has been fitted on
the coordinates in the structure file.
Options to specify input files:
-s[<.tpr/.gro/…>] (topol.tpr) (Optional)
-n[<.ndx>] (index.ndx) (Optional)
Options to specify output files:
-ol[<.xtc/.trr/…>] (lowpass.xtc) (Optional)
-oh[<.xtc/.trr/…>] (highpass.xtc) (Optional)
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
Sets the filter length as well as the output interval for low-pass filtering
Write all low-pass filtered frames
Remove jumps of atoms across the box
Fit all frames to a reference structure