1g_filter(1) GROMACS suite, VERSION 4.5 g_filter(1)
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6 g_filter - frequency filters trajectories, useful for making smooth
7 movies
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9 VERSION 4.5
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12 g_filter -f traj.xtc -s topol.tpr -n index.ndx -ol lowpass.xtc -oh
13 highpass.xtc -[no]h -[no]version -nice int -b time -e time -dt time
14 -[no]w -nf int -[no]all -[no]nojump -[no]fit
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17 g_filter performs frequency filtering on a trajectory. The filter
18 shape is cos(pi t/A) + 1 from -A to +A, where A is given by the option
19 -nf times the time step in the input trajectory. This filter reduces
20 fluctuations with period A by 85%, with period 2*A by 50% and with
21 period 3*A by 17% for low-pass filtering. Both a low-pass and
22 high-pass filtered trajectory can be written.
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25 Option -ol writes a low-pass filtered trajectory. A frame is written
26 every nf input frames. This ratio of filter length and output inter‐
27 val ensures a good suppression of aliasing of high-frequency motion,
28 which is useful for making smooth movies. Also averages of properties
29 which are linear in the coordinates are preserved, since all input
30 frames are weighted equally in the output. When all frames are needed,
31 use the -all option.
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34 Option -oh writes a high-pass filtered trajectory. The high-pass fil‐
35 tered coordinates are added to the coordinates from the structure file.
36 When using high-pass filtering use -fit or make sure you use a trajec‐
37 tory which has been fitted on the coordinates in the structure file.
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40 -f traj.xtc Input
41 Trajectory: xtc trr trj gro g96 pdb cpt
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43 -s topol.tpr Input, Opt.
44 Structure+mass(db): tpr tpb tpa gro g96 pdb
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46 -n index.ndx Input, Opt.
47 Index file
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49 -ol lowpass.xtc Output, Opt.
50 Trajectory: xtc trr trj gro g96 pdb
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52 -oh highpass.xtc Output, Opt.
53 Trajectory: xtc trr trj gro g96 pdb
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57 -[no]hno
58 Print help info and quit
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60 -[no]versionno
61 Print version info and quit
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63 -nice int 19
64 Set the nicelevel
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66 -b time 0
67 First frame (ps) to read from trajectory
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69 -e time 0
70 Last frame (ps) to read from trajectory
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72 -dt time 0
73 Only use frame when t MOD dt = first time (ps)
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75 -[no]wno
76 View output xvg, xpm, eps and pdb files
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78 -nf int 10
79 Sets the filter length as well as the output interval for low-pass
80 filtering
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82 -[no]allno
83 Write all low-pass filtered frames
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85 -[no]nojumpyes
86 Remove jumps of atoms across the box
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88 -[no]fitno
89 Fit all frames to a reference structure
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93 gromacs(7)
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95 More information about GROMACS is available at <http://www.gro‐
96 macs.org/>.
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100 Thu 26 Aug 2010 g_filter(1)