.TH g_select 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_select - selects groups of atoms based on flexible textual selections .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_select\fP .BI "\-f" " traj.xtc " .BI "\-s" " topol.tpr " .BI "\-sf" " selection.dat " .BI "\-n" " index.ndx " .BI "\-os" " size.xvg " .BI "\-oc" " cfrac.xvg " .BI "\-oi" " index.dat " .BI "\-om" " mask.dat " .BI "\-on" " index.ndx " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-b" " time " .BI "\-e" " time " .BI "\-dt" " time " .BI "\-xvg" " enum " .BI "\-[no]rmpbc" "" .BI "\-[no]pbc" "" .BI "\-select" " string " .BI "\-selrpos" " enum " .BI "\-seltype" " enum " .BI "\-[no]dump" "" .BI "\-[no]norm" "" .BI "\-[no]cfnorm" "" .BI "\-resnr" " enum " .SH DESCRIPTION \&\fB g_select\fR writes out basic data about dynamic selections. \&It can be used for some simple analyses, or the output can \&be combined with output from other programs and/or external \&analysis programs to calculate more complex things. \&Any combination of the output options is possible, but note \&that \fB \-om\fR only operates on the first selection. \&With \fB \-os\fR, calculates the number of positions in each \&selection for each frame. With \fB \-norm\fR, the output is \&between 0 and 1 and describes the fraction from the maximum \&number of positions (e.g., for selection 'resname RA and x 5' \&the maximum number of positions is the number of atoms in \&RA residues). With \fB \-cfnorm\fR, the output is divided \&by the fraction covered by the selection. \&\fB \-norm\fR and \fB \-cfnorm\fR can be specified independently \&of one another. \&With \fB \-oc\fR, the fraction covered by each selection is \&written out as a function of time. \&With \fB \-oi\fR, the selected atoms/residues/molecules are \&written out as a function of time. In the output, the first \&column contains the frame time, the second contains the number \&of positions, followed by the atom/residue/molecule numbers. \&If more than one selection is specified, the size of the second \&group immediately follows the last number of the first group \&and so on. With \fB \-dump\fR, the frame time and the number \&of positions is omitted from the output. In this case, only one \&selection can be given. \&With \fB \-on\fR, the selected atoms are written as a index file \&compatible with \fB make_ndx\fR and the analyzing tools. Each selection \&is written as a selection group and for dynamic selections a \&group is written for each frame. \&For residue numbers, the output of \fB \-oi\fR can be controlled \&with \fB \-resnr\fR: \fB number\fR (default) prints the residue \&numbers as they appear in the input file, while \fB index\fR prints \&unique numbers assigned to the residues in the order they appear \&in the input file, starting with 1. The former is more intuitive, \&but if the input contains multiple residues with the same number, \&the output can be less useful. \&With \fB \-om\fR, a mask is printed for the first selection \&as a function of time. Each line in the output corresponds to \&one frame, and contains either 0/1 for each atom/residue/molecule \&possibly selected. 1 stands for the atom/residue/molecule being \&selected for the current frame, 0 for not selected. \&With \fB \-dump\fR, the frame time is omitted from the output. .SH FILES .BI "\-f" " traj.xtc" .B Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt .BI "\-s" " topol.tpr" .B Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb .BI "\-sf" " selection.dat" .B Input, Opt. Generic data file .BI "\-n" " index.ndx" .B Input, Opt. Index file .BI "\-os" " size.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-oc" " cfrac.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-oi" " index.dat" .B Output, Opt. Generic data file .BI "\-om" " mask.dat" .B Output, Opt. Generic data file .BI "\-on" " index.ndx" .B Output, Opt. Index file .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 19" Set the nicelevel .BI "\-b" " time" " 0 " First frame (ps) to read from trajectory .BI "\-e" " time" " 0 " Last frame (ps) to read from trajectory .BI "\-dt" " time" " 0 " Only use frame when t MOD dt = first time (ps) .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-[no]rmpbc" "yes " Make molecules whole for each frame .BI "\-[no]pbc" "yes " Use periodic boundary conditions for distance calculation .BI "\-select" " string" " " Selection string (use 'help' for help) .BI "\-selrpos" " enum" " atom" Selection reference position: \fB atom\fR, \fB res_com\fR, \fB res_cog\fR, \fB mol_com\fR, \fB mol_cog\fR, \fB whole_res_com\fR, \fB whole_res_cog\fR, \fB whole_mol_com\fR, \fB whole_mol_cog\fR, \fB part_res_com\fR, \fB part_res_cog\fR, \fB part_mol_com\fR, \fB part_mol_cog\fR, \fB dyn_res_com\fR, \fB dyn_res_cog\fR, \fB dyn_mol_com\fR or \fB dyn_mol_cog\fR .BI "\-seltype" " enum" " atom" Default analysis positions: \fB atom\fR, \fB res_com\fR, \fB res_cog\fR, \fB mol_com\fR, \fB mol_cog\fR, \fB whole_res_com\fR, \fB whole_res_cog\fR, \fB whole_mol_com\fR, \fB whole_mol_cog\fR, \fB part_res_com\fR, \fB part_res_cog\fR, \fB part_mol_com\fR, \fB part_mol_cog\fR, \fB dyn_res_com\fR, \fB dyn_res_cog\fR, \fB dyn_mol_com\fR or \fB dyn_mol_cog\fR .BI "\-[no]dump" "no " Do not print the frame time (\-om, \-oi) or the index size (\-oi) .BI "\-[no]norm" "no " Normalize by total number of positions with \-os .BI "\-[no]cfnorm" "no " Normalize by covered fraction with \-os .BI "\-resnr" " enum" " number" Residue number output type: \fB number\fR or \fB index\fR .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.