g_select(1)

1g_select(1)               GROMACS suite, VERSION 4.5               g_select(1)
2
3
4

NAME

6       g_select - selects groups of atoms based on flexible textual selections
7
8       VERSION 4.5
9

SYNOPSIS

11       g_select  -f  traj.xtc  -s topol.tpr -sf selection.dat -n index.ndx -os
12       size.xvg -oc cfrac.xvg -oi index.dat -om mask.dat -on index.ndx  -[no]h
13       -[no]version  -nice  int  -b time -e time -dt time -xvg enum -[no]rmpbc
14       -[no]pbc -select string -selrpos enum -seltype enum -[no]dump -[no]norm
15       -[no]cfnorm -resnr enum
16

DESCRIPTION

18       g_select  writes  out  basic  data about dynamic selections.  It can be
19       used for some simple analyses, or the output can be combined with  out‐
20       put  from other programs and/or external analysis programs to calculate
21       more complex things.  Any combination of the output options  is  possi‐
22       ble, but note that  -om only operates on the first selection.
23
24
25       With   -os,  calculates  the  number of positions in each selection for
26       each frame. With  -norm, the output is between 0 and  1  and  describes
27       the  fraction from the maximum number of positions (e.g., for selection
28       'resname RA and x  5' the maximum number of positions is the number  of
29       atoms  in  RA  residues).  With   -cfnorm, the output is divided by the
30       fraction covered by the selection.   -norm and  -cfnorm can  be  speci‐
31       fied independently of one another.
32
33
34       With   -oc,  the fraction covered by each selection is written out as a
35       function of time.
36
37
38       With  -oi, the selected atoms/residues/molecules are written out  as  a
39       function  of  time.  In the output, the first column contains the frame
40       time, the second contains the number  of  positions,  followed  by  the
41       atom/residue/molecule  numbers.   If  more than one selection is speci‐
42       fied, the size of the second group immediately follows the last  number
43       of  the first group and so on. With  -dump, the frame time and the num‐
44       ber of positions is omitted from the output. In  this  case,  only  one
45       selection can be given.
46
47
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.
52
53
54       For residue numbers, the output of  -oi can be controlled with  -resnr:
55       number (default) prints the residue numbers as they appear in the input
56       file, while  index prints unique numbers assigned to  the  residues  in
57       the order they appear in the input file, starting with 1. The former is
58       more intuitive, but if the input contains multiple  residues  with  the
59       same number, the output can be less useful.
60
61
62       With   -om,  a mask is printed for the first selection as a function of
63       time. Each line in the output corresponds to one  frame,  and  contains
64       either  0/1  for each atom/residue/molecule possibly selected. 1 stands
65       for the atom/residue/molecule being selected for the current  frame,  0
66       for not selected.  With  -dump, the frame time is omitted from the out‐
67       put.
68

FILES

70       -f traj.xtc Input, Opt.
71        Trajectory: xtc trr trj gro g96 pdb cpt
72
73       -s topol.tpr Input, Opt.
74        Structure+mass(db): tpr tpb tpa gro g96 pdb
75
76       -sf selection.dat Input, Opt.
77        Generic data file
78
79       -n index.ndx Input, Opt.
80        Index file
81
82       -os size.xvg Output, Opt.
83        xvgr/xmgr file
84
85       -oc cfrac.xvg Output, Opt.
86        xvgr/xmgr file
87
88       -oi index.dat Output, Opt.
89        Generic data file
90
91       -om mask.dat Output, Opt.
92        Generic data file
93
94       -on index.ndx Output, Opt.
95        Index file
96
97

OTHER OPTIONS

99       -[no]hno
100        Print help info and quit
101
102       -[no]versionno
103        Print version info and quit
104
105       -nice int 19
106        Set the nicelevel
107
108       -b time 0
109        First frame (ps) to read from trajectory
110
111       -e time 0
112        Last frame (ps) to read from trajectory
113
114       -dt time 0
115        Only use frame when t MOD dt = first time (ps)
116
117       -xvg enum xmgrace
118        xvg plot formatting:  xmgrace,  xmgr or  none
119
120       -[no]rmpbcyes
121        Make molecules whole for each frame
122
123       -[no]pbcyes
124        Use periodic boundary conditions for distance calculation
125
126       -select string
127        Selection string (use 'help' for help)
128
129       -selrpos enum atom
130        Selection reference position:   atom,   res_com,   res_cog,   mol_com,
131       mol_cog,       whole_res_com,       whole_res_cog,       whole_mol_com,
132       whole_mol_cog,      part_res_com,      part_res_cog,      part_mol_com,
133       part_mol_cog,  dyn_res_com,  dyn_res_cog,  dyn_mol_com or  dyn_mol_cog
134
135       -seltype enum atom
136        Default  analysis  positions:   atom,   res_com,   res_cog,   mol_com,
137       mol_cog,       whole_res_com,       whole_res_cog,       whole_mol_com,
138       whole_mol_cog,      part_res_com,      part_res_cog,      part_mol_com,
139       part_mol_cog,  dyn_res_com,  dyn_res_cog,  dyn_mol_com or  dyn_mol_cog
140
141       -[no]dumpno
142        Do not print the frame time (-om, -oi) or the index size (-oi)
143
144       -[no]normno
145        Normalize by total number of positions with -os
146
147       -[no]cfnormno
148        Normalize by covered fraction with -os
149
150       -resnr enum number
151        Residue number output type:  number or  index
152
153

NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO