Section 1: user commands and tools
NAME g_bundle – analyzes bundles of axes, e.g. helices VERSION 4.0.1 SYNOPSIS g_bundle -f traj.xtc -s topol.tpr -n index.ndx -ol bun_len.xvg -od bun_dist.xvg -oz bun_z.xvg -ot bun_tilt.xvg -otr bun_tiltr.xvg -otl bun_tiltl.xvg -ok bun_kink.xvg -okr bun_kinkr.xvg -okl bun_kinkl.xvg -oa axes.pdb -[no]h -nice int -b time -e time -dt time -tu enum -[no]xvgr -na int -[no]z DESCRIPTION…
NAME g_bundle – analyzes bundles of axes, e.g. helices VERSION 4.0.1 SYNOPSIS g_bundle -f traj.xtc -s topol.tpr -n index.ndx -ol bun_len.xvg -od bun_dist.xvg -oz bun_z.xvg -ot bun_tilt.xvg -otr bun_tiltr.xvg -otl bun_tiltl.xvg -ok bun_kink.xvg -okr bun_kinkr.xvg -okl bun_kinkl.xvg -oa axes.pdb -[no]h -nice int -b time -e time -dt time -tu enum -[no]xvgr -na int -[no]z DESCRIPTION…
NAME g_bond – calculates distances between atoms VERSION 4.0.1 SYNOPSIS g_bond -f traj.xtc -n index.ndx -s topol.tpr -o bonds.xvg -l bonds.log -d distance.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -blen real -tol real -[no]aver -[no]averdist DESCRIPTION g_bond makes a distribution of bond lengths. If all is well a gaussian distribution…
NAME g_bond – calculates distances between atoms VERSION 4.0.1 SYNOPSIS g_bond -f traj.xtc -n index.ndx -s topol.tpr -o bonds.xvg -l bonds.log -d distance.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -blen real -tol real -[no]aver -[no]averdist DESCRIPTION g_bond makes a distribution of bond lengths. If all is well a gaussian distribution…
NAME g_angle – calculates distributions and correlations for angles and dihedrals VERSION 4.0.1 SYNOPSIS g_angle -f traj.xtc -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oh trhisto.xvg -oc dihcorr.xvg -or traj.trr -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -type enum -[no]all -binwidth real -[no]periodic -[no]chandler -[no]avercorr -acflen int -[no]normalize…
NAME g_angle – calculates distributions and correlations for angles and dihedrals VERSION 4.0.1 SYNOPSIS g_angle -f traj.xtc -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oh trhisto.xvg -oc dihcorr.xvg -or traj.trr -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -type enum -[no]all -binwidth real -[no]periodic -[no]chandler -[no]avercorr -acflen int -[no]normalize…
NAME g_analyze – analyzes data sets VERSION 4.0.1 SYNOPSIS g_analyze -f graph.xvg -ac autocorr.xvg -msd msd.xvg -cc coscont.xvg -dist distr.xvg -av average.xvg -ee errest.xvg -g fitlog.log -[no]h -nice int -[no]w -[no]xvgr -[no]time -b real -e real -n int -[no]d -bw real -errbar enum -[no]integrate -aver_start real -[no]xydy -[no]regression -[no]luzar -temp real -fitstart real -smooth real…
NAME g_analyze – analyzes data sets VERSION 4.0.1 SYNOPSIS g_analyze -f graph.xvg -ac autocorr.xvg -msd msd.xvg -cc coscont.xvg -dist distr.xvg -av average.xvg -ee errest.xvg -g fitlog.log -[no]h -nice int -[no]w -[no]xvgr -[no]time -b real -e real -n int -[no]d -bw real -errbar enum -[no]integrate -aver_start real -[no]xydy -[no]regression -[no]luzar -temp real -fitstart real -smooth real…
NAME g_anaeig – analyzes the eigenvectors VERSION 4.0.1 SYNOPSIS g_anaeig -v eigenvec.trr -v2 eigenvec2.trr -f traj.xtc -s topol.tpr -n index.ndx -eig eigenval.xvg -eig2 eigenval2.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -proj proj.xvg -2d 2dproj.xvg -3d 3dproj.pdb -filt filtered.xtc -extr extreme.pdb -over overlap.xvg -inpr inprod.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr…
NAME g_anaeig – analyzes the eigenvectors VERSION 4.0.1 SYNOPSIS g_anaeig -v eigenvec.trr -v2 eigenvec2.trr -f traj.xtc -s topol.tpr -n index.ndx -eig eigenval.xvg -eig2 eigenval2.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -proj proj.xvg -2d 2dproj.xvg -3d 3dproj.pdb -filt filtered.xtc -extr extreme.pdb -over overlap.xvg -inpr inprod.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr…
NAME anadock – cluster structures from Autodock runs VERSION 4.0.1 SYNOPSIS anadock -f eiwit.pdb -ox cluster.pdb -od edocked.xvg -of efree.xvg -g anadock.log -[no]h -nice int -[no]xvgr -[no]free -[no]rms -cutoff real DESCRIPTION anadock analyses the results of an Autodock run and clusters the structures together, based on distance or RMSD. The docked energy and free energy…
NAME anadock – cluster structures from Autodock runs VERSION 4.0.1 SYNOPSIS anadock -f eiwit.pdb -ox cluster.pdb -od edocked.xvg -of efree.xvg -g anadock.log -[no]h -nice int -[no]xvgr -[no]free -[no]rms -cutoff real DESCRIPTION anadock analyses the results of an Autodock run and clusters the structures together, based on distance or RMSD. The docked energy and free energy…
NAME g3topbm – convert a Group 3 fax file into a portable bitmap SYNOPSIS g3topbm [-kludge] [-reversebits] [-stretch] [g3file] DESCRIPTION Reads a Group 3 fax file as input. Produces a portable bitmap as output. OPTIONS -kludge Tells g3topbm to ignore the first few lines of the file; sometimes fax files have some junk at the…
NAME g3data – A tool for extracting data from graphs. SYNOPSIS g3data [ -max x y ] [ -scale factor ] [ -coords llx lly rux ruy ] [ -errors ] [ -lnx ] [ -lny ] [ filename(s) … ] DESCRIPTION g3data is a tool for extracting data from scanned graphs. For graphs published…
NAME g3cat – concatenate multiple g3 documents SYNOPSIS g3cat [-l] [-a] g3-file1 … DESCRIPTION g3cat concatenates g3 files. These can either be ‘raw’, that is, bitmaps packed according to the CCITT T.4 standard for one-dimensional bitmap encoding, or ‘digifax’ files, created by GNU’s GhostScript package with the digifax drivers. Its output is a concatenation of…
NAME g32pbm – convert a Group 3 fax file into a portable bitmap SYNOPSIS g32pbm [-reversebits] [-stretch] [g3file] DESCRIPTION Reads a Group 3 fax file (raw or digifax) as input. If no filename is given, stdin is used. Produces a portable bitmap as output. OPTIONS -r Tells g32pbm to interpret bits least-significant first, instead of…
NAME g2root – convert GEANT geometry files to ROOT files SYNOPSIS g2rootd [-f map_name] geant_name macro_name DESCRIPTION You can convert a GEANT (see http://geant.cern.ch/ fore more on GEANT) geometry to ROOT geometry with the following steps 1 Run the interactive version of GEANT and produce a Zebra RZ file detector.geom, by typing the command: Geant…
NAME g-ir-scanner – extracting C metadata from sources and headers SYNOPSIS g-ir-scanner [OPTION…] FILES… DESCRIPTION g-ir-scanner is a tool which generates GIR XML files by parsing headers and introspecting GObject based libraries. It is usually invoked during the normal build step for a project and the information is saved to disk and later installed, so…
NAME g-ir-generate – typelib generator SYNOPSIS g-ir-generate [OPTION…] FILES… DESCRIPTION g-ir-generate is an GIR generator, using the repository API. It generates GIR files from a raw typelib or in a shared library (–shlib). The output will be written to standard output unless the –output is specified. OPTIONS , –help Show help options , –shlib=FILENAME The…
NAME g-ir-compiler – typelib compiler. SYNOPSIS g-ir-compiler [OPTION…] GIRFILE DESCRIPTION g-ir-compiler converts one or more GIR files into one or more typelib. The output will be written to standard output unless the –output is specified. OPTIONS –help Show help options –output=FILENAME Save the resulting output in FILENAME. –verbose Show verbose messages –debug Show debug messages…