1GMX-SELECT(1) GROMACS GMX-SELECT(1)
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6 gmx-select - Print general information about selections
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9 gmx select [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10 [-os [<.xvg>]] [-oc [<.xvg>]] [-oi [<.dat>]]
11 [-on [<.ndx>]] [-om [<.xvg>]] [-of [<.xvg>]]
12 [-ofpdb [<.pdb>]] [-olt [<.xvg>]] [-b <time>] [-e <time>]
13 [-dt <time>] [-tu <enum>] [-fgroup <selection>]
14 [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
15 [-selrpos <enum>] [-seltype <enum>] [-select <selection>]
16 [-[no]norm] [-[no]cfnorm] [-resnr <enum>]
17 [-pdbatoms <enum>] [-[no]cumlt]
18
20 gmx select writes out basic data about dynamic selections. It can be
21 used for some simple analyses, or the output can be combined with out‐
22 put from other programs and/or external analysis programs to calculate
23 more complex things. For detailed help on the selection syntax, please
24 use gmx help selections.
25 Any combination of the output options is possible, but note that -om
27 only operates on the first selection. Also note that if you provide no
28 output options, no output is produced.
29 With -os, calculates the number of positions in each selection for each
31 frame. With -norm, the output is between 0 and 1 and describes the
32 fraction from the maximum number of positions (e.g., for selection
33 'resname RA and x < 5' the maximum number of positions is the number of
34 atoms in RA residues). With -cfnorm, the output is divided by the frac‐
35 tion covered by the selection. -norm and -cfnorm can be specified in‐
36 dependently of one another.
37 With -oc, the fraction covered by each selection is written out as a
39 function of time.
40 With -oi, the selected atoms/residues/molecules are written out as a
42 function of time. In the output, the first column contains the frame
43 time, the second contains the number of positions, followed by the
44 atom/residue/molecule numbers. If more than one selection is speci‐
45 fied, the size of the second group immediately follows the last number
46 of the first group and so on.
47 With -on, the selected atoms are written as a index file compatible
49 with make_ndx and the analyzing tools. Each selection is written as a
50 selection group and for dynamic selections a group is written for each
51 frame.
52 For residue numbers, the output of -oi can be controlled with -resnr:
54 number (default) prints the residue numbers as they appear in the input
55 file, while index prints unique numbers assigned to the residues in the
56 order they appear in the input file, starting with 1. The former is
57 more intuitive, but if the input contains multiple residues with the
58 same number, the output can be less useful.
59 With -om, a mask is printed for the first selection as a function of
61 time. Each line in the output corresponds to one frame, and contains
62 either 0/1 for each atom/residue/molecule possibly selected. 1 stands
63 for the atom/residue/molecule being selected for the current frame, 0
64 for not selected.
65 With -of, the occupancy fraction of each position (i.e., the fraction
67 of frames where the position is selected) is printed.
68 With -ofpdb, a PDB file is written out where the occupancy column is
70 filled with the occupancy fraction of each atom in the selection. The
71 coordinates in the PDB file will be those from the input topology.
72 -pdbatoms can be used to control which atoms appear in the output PDB
73 file: with all all atoms are present, with maxsel all atoms possibly
74 selected by the selection are present, and with selected only atoms
75 that are selected at least in one frame are present.
76 With -olt, a histogram is produced that shows the number of selected
78 positions as a function of the time the position was continuously se‐
79 lected. -cumlt can be used to control whether subintervals of longer
80 intervals are included in the histogram.
81 -om, -of, and -olt only make sense with dynamic selections.
83 To plot coordinates for selections, use gmx trajectory.
85
87 Options to specify input files:
88 -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
90 Input trajectory or single configuration: xtc trr cpt gro g96
91 pdb tng
92 -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
94 Input structure: tpr gro g96 pdb brk ent
95 -n [<.ndx>] (index.ndx) (Optional)
97 Extra index groups
98 Options to specify output files:
100 -os [<.xvg>] (size.xvg) (Optional)
102 Number of positions in each selection
103 -oc [<.xvg>] (cfrac.xvg) (Optional)
105 Covered fraction for each selection
106 -oi [<.dat>] (index.dat) (Optional)
108 Indices selected by each selection
109 -on [<.ndx>] (index.ndx) (Optional)
111 Index file from the selection
112 -om [<.xvg>] (mask.xvg) (Optional)
114 Mask for selected positions
115 -of [<.xvg>] (occupancy.xvg) (Optional)
117 Occupied fraction for selected positions
118 -ofpdb [<.pdb>] (occupancy.pdb) (Optional)
120 PDB file with occupied fraction for selected positions
121 -olt [<.xvg>] (lifetime.xvg) (Optional)
123 Lifetime histogram
124 Other options:
126 -b <time> (0)
128 First frame (ps) to read from trajectory
129 -e <time> (0)
131 Last frame (ps) to read from trajectory
132 -dt <time> (0)
134 Only use frame if t MOD dt == first time (ps)
135 -tu <enum> (ps)
137 Unit for time values: fs, ps, ns, us, ms, s
138 -fgroup <selection>
140 Atoms stored in the trajectory file (if not set, assume first N
141 atoms)
142 -xvg <enum> (xmgrace)
144 Plot formatting: xmgrace, xmgr, none
145 -[no]rmpbc (yes)
147 Make molecules whole for each frame
148 -[no]pbc (yes)
150 Use periodic boundary conditions for distance calculation
151 -sf <file>
153 Provide selections from files
154 -selrpos <enum> (atom)
156 Selection reference positions: atom, res_com, res_cog, mol_com,
157 mol_cog, whole_res_com, whole_res_cog, whole_mol_com,
158 whole_mol_cog, part_res_com, part_res_cog, part_mol_com,
159 part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
160 -seltype <enum> (atom)
162 Default selection output positions: atom, res_com, res_cog,
163 mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com,
164 whole_mol_cog, part_res_com, part_res_cog, part_mol_com,
165 part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
166 -select <selection>
168 Selections to analyze
169 -[no]norm (no)
171 Normalize by total number of positions with -os
172 -[no]cfnorm (no)
174 Normalize by covered fraction with -os
175 -resnr <enum> (number)
177 Residue number output type with -oi and -on: number, index
178 -pdbatoms <enum> (all)
180 Atoms to write with -ofpdb: all, maxsel, selected
181 -[no]cumlt (yes)
183 Cumulate subintervals of longer intervals in -olt
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186 gmx(1)
187 More information about GROMACS is available at <‐
189 http://www.gromacs.org/>.
190
192 2022, GROMACS development team
1932022.3 Sep 02, 2022 GMX-SELECT(1)