1GMX-FILTER(1)                       GROMACS                      GMX-FILTER(1)
2
3
4

NAME

6       gmx-filter  -  Frequency  filter trajectories, useful for making smooth
7       movies
8

SYNOPSIS

10          gmx filter [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
11                     [-ol [<.xtc/.trr/...>]] [-oh [<.xtc/.trr/...>]]
12                     [-b <time>] [-e <time>] [-dt <time>] [-[no]w] [-nf <int>]
13                     [-[no]all] [-[no]nojump] [-[no]fit]
14

DESCRIPTION

16       gmx filter performs frequency filtering on a  trajectory.   The  filter
17       shape  is cos(pi t/A) + 1 from -A to +A, where A is given by the option
18       -nf times the time step in the input trajectory.  This  filter  reduces
19       fluctuations  with  period  A  by  85%, with period 2*A by 50% and with
20       period 3*A  by  17%  for  low-pass  filtering.   Both  a  low-pass  and
21       high-pass filtered trajectory can be written.
22
23       Option  -ol  writes a low-pass filtered trajectory.  A frame is written
24       every -nf input frames.  This ratio of filter length and output  inter‐
25       val  ensures  a  good suppression of aliasing of high-frequency motion,
26       which is useful for making smooth movies. Also averages  of  properties
27       which  are  linear  in  the  coordinates are preserved, since all input
28       frames are weighted equally in the output.  When all frames are needed,
29       use the -all option.
30
31       Option  -oh writes a high-pass filtered trajectory.  The high-pass fil‐
32       tered coordinates are added to the coordinates from the structure file.
33       When  using high-pass filtering use -fit or make sure you use a trajec‐
34       tory that has been fitted on the coordinates in the structure file.
35

OPTIONS

37       Options to specify input files:
38
39       -f [<.xtc/.trr/…>] (traj.xtc)
40              Trajectory: xtc trr cpt gro g96 pdb tng
41
42       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
43              Structure+mass(db): tpr gro g96 pdb brk ent
44
45       -n [<.ndx>] (index.ndx) (Optional)
46              Index file
47
48       Options to specify output files:
49
50       -ol [<.xtc/.trr/…>] (lowpass.xtc) (Optional)
51              Trajectory: xtc trr gro g96 pdb tng
52
53       -oh [<.xtc/.trr/…>] (highpass.xtc) (Optional)
54              Trajectory: xtc trr gro g96 pdb tng
55
56       Other options:
57
58       -b <time> (0)
59              Time of first frame to read from trajectory (default unit ps)
60
61       -e <time> (0)
62              Time of last frame to read from trajectory (default unit ps)
63
64       -dt <time> (0)
65              Only use frame when t MOD dt = first time (default unit ps)
66
67       -[no]w (no)
68              View output .xvg, .xpm, .eps and .pdb files
69
70       -nf <int> (10)
71              Sets the filter length  as  well  as  the  output  interval  for
72              low-pass filtering
73
74       -[no]all (no)
75              Write all low-pass filtered frames
76
77       -[no]nojump (yes)
78              Remove jumps of atoms across the box
79
80       -[no]fit (no)
81              Fit all frames to a reference structure
82

SEE ALSO

84       gmx(1)
85
86       More     information    about    GROMACS    is    available    at    <‐
87       http://www.gromacs.org/>.
88

90       2019, GROMACS development team
91
92
93
94
952019.2                           Apr 16, 2019                    GMX-FILTER(1)
Impressum