1GMX-SELECT(1)                       GROMACS                      GMX-SELECT(1)
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NAME

6       gmx-select - Print general information about selections
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SYNOPSIS

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]
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DESCRIPTION

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
26       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
30       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.
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38       With  -oc,  the  fraction covered by each selection is written out as a
39       function of time.
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41       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.
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48       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.
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53       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
60       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
66       With  -of,  the occupancy fraction of each position (i.e., the fraction
67       of frames where the position is selected) is printed.
68
69       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.
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77       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.
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82       -om, -of, and -olt only make sense with dynamic selections.
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84       To plot coordinates for selections, use gmx trajectory.
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OPTIONS

87       Options to specify input files:
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89       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
90              Input  trajectory  or  single configuration: xtc trr cpt gro g96
91              pdb tng
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93       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
94              Input structure: tpr gro g96 pdb brk ent
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96       -n [<.ndx>] (index.ndx) (Optional)
97              Extra index groups
98
99       Options to specify output files:
100
101       -os [<.xvg>] (size.xvg) (Optional)
102              Number of positions in each selection
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104       -oc [<.xvg>] (cfrac.xvg) (Optional)
105              Covered fraction for each selection
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107       -oi [<.dat>] (index.dat) (Optional)
108              Indices selected by each selection
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110       -on [<.ndx>] (index.ndx) (Optional)
111              Index file from the selection
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113       -om [<.xvg>] (mask.xvg) (Optional)
114              Mask for selected positions
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116       -of [<.xvg>] (occupancy.xvg) (Optional)
117              Occupied fraction for selected positions
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119       -ofpdb [<.pdb>] (occupancy.pdb) (Optional)
120              PDB file with occupied fraction for selected positions
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122       -olt [<.xvg>] (lifetime.xvg) (Optional)
123              Lifetime histogram
124
125       Other options:
126
127       -b <time> (0)
128              First frame (ps) to read from trajectory
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130       -e <time> (0)
131              Last frame (ps) to read from trajectory
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133       -dt <time> (0)
134              Only use frame if t MOD dt == first time (ps)
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136       -tu <enum> (ps)
137              Unit for time values: fs, ps, ns, us, ms, s
138
139       -fgroup <selection>
140              Atoms stored in the trajectory file (if not set, assume first  N
141              atoms)
142
143       -xvg <enum> (xmgrace)
144              Plot formatting: xmgrace, xmgr, none
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146       -[no]rmpbc (yes)
147              Make molecules whole for each frame
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149       -[no]pbc (yes)
150              Use periodic boundary conditions for distance calculation
151
152       -sf <file>
153              Provide selections from files
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155       -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
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161       -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
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167       -select <selection>
168              Selections to analyze
169
170       -[no]norm (no)
171              Normalize by total number of positions with -os
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173       -[no]cfnorm (no)
174              Normalize by covered fraction with -os
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176       -resnr <enum> (number)
177              Residue number output type with -oi and -on: number, index
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179       -pdbatoms <enum> (all)
180              Atoms to write with -ofpdb: all, maxsel, selected
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182       -[no]cumlt (yes)
183              Cumulate subintervals of longer intervals in -olt
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SEE ALSO

186       gmx(1)
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188       More     information    about    GROMACS    is    available    at    <‐
189       http://www.gromacs.org/>.
190
192       2022, GROMACS development team
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1972022.3                           Sep 02, 2022                    GMX-SELECT(1)
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