This is the command gmx-filter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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)
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
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