The Linux Manuals (man pages) document is an important part of Linux documents. Linux Manuals are organized as several sections. Each section has a group of commands for a specific area in Linux usage, administration or development.
g_densmap – calculates 2D planar or axial-radial density maps VERSION 4.0.1 Synopsisg_densmap -f traj.xtc -s topol.tpr -n index.ndx -o densmap.xpm -[no]h -nice int -b time -e time -dt time -[no]w -bin real -aver enum -xmin real -xmax real -n1 int -n2 int -amax real -rmax real -[no]mirror -unit enum -dmin real -dmax real Descriptiong_densmap computes…
g_densmap – calculates 2D planar or axial-radial density maps VERSION 4.0.1 Synopsisg_densmap -f traj.xtc -s topol.tpr -n index.ndx -o densmap.xpm -[no]h -nice int -b time -e time -dt time -[no]w -bin real -aver enum -xmin real -xmax real -n1 int -n2 int -amax real -rmax real -[no]mirror -unit enum -dmin real -dmax real Descriptiong_densmap computes…
g_density – calculates the density of the system VERSION 4.0.1 Synopsisg_density -f traj.xtc -n index.ndx -s topol.tpr -ei electrons.dat -o density.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d string -sl int -dens enum -ng int -[no]symm -[no]center DescriptionCompute partial densities across the box, using an index file. Densities in kg/m3,…
g_density – calculates the density of the system VERSION 4.0.1 Synopsisg_density -f traj.xtc -n index.ndx -s topol.tpr -ei electrons.dat -o density.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d string -sl int -dens enum -ng int -[no]symm -[no]center DescriptionCompute partial densities across the box, using an index file. Densities in kg/m3,…
g_current – calculates dielectric constants for charged systems VERSION 4.0.1 Synopsisg_current -s topol.tpr -n index.ndx -f traj.xtc -o current.xvg -caf caf.xvg -dsp dsp.xvg -md md.xvg -mj mj.xvg -mc mc.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -sh int -[no]nojump -eps real -bfit real -efit real -bvit real -evit real -tr real…
g_current – calculates dielectric constants for charged systems VERSION 4.0.1 Synopsisg_current -s topol.tpr -n index.ndx -f traj.xtc -o current.xvg -caf caf.xvg -dsp dsp.xvg -md md.xvg -mj mj.xvg -mc mc.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -sh int -[no]nojump -eps real -bfit real -efit real -bvit real -evit real -tr real…
g_covar – calculates and diagonalizes the covariance matrix VERSION 4.0.1 Synopsisg_covar -f traj.xtc -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log -ascii covar.dat -xpm covar.xpm -xpma covara.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]xvgr -[no]fit -[no]ref -[no]mwa -last int -[no]pbc Description g_covar calculates and diagonalizes the…
g_covar – calculates and diagonalizes the covariance matrix VERSION 4.0.1 Synopsisg_covar -f traj.xtc -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log -ascii covar.dat -xpm covar.xpm -xpma covara.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]xvgr -[no]fit -[no]ref -[no]mwa -last int -[no]pbc Description g_covar calculates and diagonalizes the…
g_confrms – fits two structures and calculates the rmsd VERSION 4.0.1 Synopsisg_confrms -f1 conf1.gro -f2 conf2.gro -o fit.pdb -n1 fit1.ndx -n2 fit2.ndx -no match.ndx -[no]h -nice int -[no]w -[no]one -[no]mw -[no]pbc -[no]fit -[no]name -[no]label -[no]bfac Descriptiong_confrms computes the root mean square deviation (RMSD) of two structures after LSQ fitting the second structure on the first…
g_confrms – fits two structures and calculates the rmsd VERSION 4.0.1 Synopsisg_confrms -f1 conf1.gro -f2 conf2.gro -o fit.pdb -n1 fit1.ndx -n2 fit2.ndx -no match.ndx -[no]h -nice int -[no]w -[no]one -[no]mw -[no]pbc -[no]fit -[no]name -[no]label -[no]bfac Descriptiong_confrms computes the root mean square deviation (RMSD) of two structures after LSQ fitting the second structure on the first…
g_clustsize – calculate size distributions of atomic clusters VERSION 4.0.1 Synopsisg_clustsize -f traj.xtc -s topol.tpr -n index.ndx -o csize.xpm -ow csizew.xpm -nc nclust.xvg -mc maxclust.xvg -ac avclust.xvg -hc histo-clust.xvg -temp temp.xvg -mcn maxclust.ndx -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -cut real -[no]mol -[no]pbc -nskip int -nlevels int -ndf…
g_clustsize – calculate size distributions of atomic clusters VERSION 4.0.1 Synopsisg_clustsize -f traj.xtc -s topol.tpr -n index.ndx -o csize.xpm -ow csizew.xpm -nc nclust.xvg -mc maxclust.xvg -ac avclust.xvg -hc histo-clust.xvg -temp temp.xvg -mcn maxclust.ndx -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -cut real -[no]mol -[no]pbc -nskip int -nlevels int -ndf…
g_cluster – clusters structures VERSION 4.0.1 Synopsisg_cluster -f traj.xtc -s topol.tpr -n index.ndx -dm rmsd.xpm -o rmsd-clust.xpm -g cluster.log -dist rmsd-dist.xvg -ev rmsd-eig.xvg -sz clust-size.xvg -tr clust-trans.xpm -ntr clust-trans.xvg -clid clust-id.xvg -cl clusters.pdb -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -[no]dista -nlevels int -cutoff real -[no]fit -max real -skip…
g_cluster – clusters structures VERSION 4.0.1 Synopsisg_cluster -f traj.xtc -s topol.tpr -n index.ndx -dm rmsd.xpm -o rmsd-clust.xpm -g cluster.log -dist rmsd-dist.xvg -ev rmsd-eig.xvg -sz clust-size.xvg -tr clust-trans.xpm -ntr clust-trans.xvg -clid clust-id.xvg -cl clusters.pdb -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -[no]dista -nlevels int -cutoff real -[no]fit -max real -skip…
g_chi – calculates everything you want to know about chi and other dihedrals VERSION 4.0.1 Synopsisg_chi -s conf.gro -f traj.xtc -o order.xvg -p order.pdb -ss ssdump.dat -jc Jcoupling.xvg -corr dihcorr.xvg -g chi.log -ot dihtrans.xvg -oh trhisto.xvg -rt restrans.xvg -cp chiprodhisto.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -r0 int -[no]phi -[no]psi…
g_chi – calculates everything you want to know about chi and other dihedrals VERSION 4.0.1 Synopsisg_chi -s conf.gro -f traj.xtc -o order.xvg -p order.pdb -ss ssdump.dat -jc Jcoupling.xvg -corr dihcorr.xvg -g chi.log -ot dihtrans.xvg -oh trhisto.xvg -rt restrans.xvg -cp chiprodhisto.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -r0 int -[no]phi -[no]psi…
g_bundle – analyzes bundles of axes, e.g. helices VERSION 4.0.1 Synopsisg_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 Descriptiong_bundle analyzes bundles…
g_bundle – analyzes bundles of axes, e.g. helices VERSION 4.0.1 Synopsisg_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 Descriptiong_bundle analyzes bundles…
g_bond – calculates distances between atoms VERSION 4.0.1 Synopsisg_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 Descriptiong_bond makes a distribution of bond lengths. If all is well a gaussian distribution should be made…
g_bond – calculates distances between atoms VERSION 4.0.1 Synopsisg_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 Descriptiong_bond makes a distribution of bond lengths. If all is well a gaussian distribution should be made…