gmx-filter(1) GROMACS Manual gmx-filter(1)NAMEgmx-filter - Frequency filter trajectories, useful for making smooth
movies
SYNOPSIS
gmx filter [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-ol [<.xtc/.trr/...>]]
[-oh [<.xtc/.trr/...>]] [-nice <int>] [-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 fil‐
tered coordinates are added to the coordinates from the structure file.
When using high-pass filtering use -fit or make sure you use a trajec‐
tory that has been fitted on the coordinates in the structure file.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-ol [<.xtc/.trr/...>] (lowpass.xtc) (Output, Optional)
Trajectory: xtc trr trj gro g96 pdb tng
-oh [<.xtc/.trr/...>] (highpass.xtc) (Output, Optional)
Trajectory: xtc trr trj gro g96 pdb tng
Other options:
-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 (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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-filter(1)