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gmx-filter(1)			GROMACS Manual			 gmx-filter(1)

NAME
       gmx-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 ALSO
       gromacs(7)

       More   information  about  GROMACS  is  available  at  <http://www.gro‐
       macs.org/>.

VERSION 5.0.6							 gmx-filter(1)

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