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.
NAME sigeps – convert c6/12 or c6/cn combinations to and from sigma/epsilon VERSION 4.0.1 SYNOPSIS sigeps -o potje.xvg -[no]h -nice int -[no]w -[no]xvgr -c6 real -cn real -pow int -sig real -eps real -A real -B real -C real -qi real -qj real -sigfac real DESCRIPTION Sigeps is a simple utility that converts c6/c12 or…
NAME g_sham – read/write xmgr and xvgr data sets VERSION 4.0.1 SYNOPSIS g_sham -f graph.xvg -ge gibbs.xvg -ene esham.xvg -dist ener.xvg -histo edist.xvg -bin bindex.ndx -lp prob.xpm -ls gibbs.xpm -lsh enthalpy.xpm -lss entropy.xpm -map map.xpm -ls3 gibbs3.pdb -mdata mapdata.xvg -g shamlog.log -[no]h -nice int -[no]w -[no]xvgr -[no]time -b real -e real -ttol real -n int…
NAME g_sham – read/write xmgr and xvgr data sets VERSION 4.0.1 SYNOPSIS g_sham -f graph.xvg -ge gibbs.xvg -ene esham.xvg -dist ener.xvg -histo edist.xvg -bin bindex.ndx -lp prob.xpm -ls gibbs.xpm -lsh enthalpy.xpm -lss entropy.xpm -map map.xpm -ls3 gibbs3.pdb -mdata mapdata.xvg -g shamlog.log -[no]h -nice int -[no]w -[no]xvgr -[no]time -b real -e real -ttol real -n int…
NAME g_sgangle – computes the angle and distance between two groups VERSION 4.0.1 SYNOPSIS g_sgangle -f traj.xtc -n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]one -[no]z DESCRIPTION Compute the angle and distance between two groups. The groups are defined…
NAME g_sgangle – computes the angle and distance between two groups VERSION 4.0.1 SYNOPSIS g_sgangle -f traj.xtc -n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]one -[no]z DESCRIPTION Compute the angle and distance between two groups. The groups are defined…
NAME g_sdf – calculates the spatial distribution function (faster than g_spatial) VERSION 4.0.1 SYNOPSIS g_sdf -f traj.xtc -n index.ndx -s topol.tpr -o gom_plt.dat -r refmol.gro -[no]h -nice int -b time -e time -dt time -mode int -triangle vector -dtri vector -bin real -grid vector DESCRIPTION g_sdf calculates the spatial distribution function (SDF) of a set…
NAME g_sdf – calculates the spatial distribution function (faster than g_spatial) VERSION 4.0.1 SYNOPSIS g_sdf -f traj.xtc -n index.ndx -s topol.tpr -o gom_plt.dat -r refmol.gro -[no]h -nice int -b time -e time -dt time -mode int -triangle vector -dtri vector -bin real -grid vector DESCRIPTION g_sdf calculates the spatial distribution function (SDF) of a set…
NAME g_sas – computes solvent accessible surface area VERSION 4.0.1 SYNOPSIS g_sas -f traj.xtc -s topol.tpr -o area.xvg -or resarea.xvg -oa atomarea.xvg -tv volume.xvg -q connelly.pdb -n index.ndx -i surfat.itp -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -probe real -ndots int -qmax real -[no]f_index -minarea real -[no]pbc -[no]prot -dgs real DESCRIPTION…
NAME g_sas – computes solvent accessible surface area VERSION 4.0.1 SYNOPSIS g_sas -f traj.xtc -s topol.tpr -o area.xvg -or resarea.xvg -oa atomarea.xvg -tv volume.xvg -q connelly.pdb -n index.ndx -i surfat.itp -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -probe real -ndots int -qmax real -[no]f_index -minarea real -[no]pbc -[no]prot -dgs real DESCRIPTION…
NAME g_saltbr – computes salt bridges VERSION 4.0.1 SYNOPSIS g_saltbr -f traj.xtc -s topol.tpr -[no]h -nice int -b time -e time -dt time -t real -[no]sep DESCRIPTION g_saltbr plots the distance between all combination of charged groups as a function of time. The groups are combined in different ways.A minimum distance can be given, (eg….
NAME g_saltbr – computes salt bridges VERSION 4.0.1 SYNOPSIS g_saltbr -f traj.xtc -s topol.tpr -[no]h -nice int -b time -e time -dt time -t real -[no]sep DESCRIPTION g_saltbr plots the distance between all combination of charged groups as a function of time. The groups are combined in different ways.A minimum distance can be given, (eg….
NAME g_rotacf – calculates the rotational correlation function for molecules VERSION 4.0.1 SYNOPSIS g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]d -[no]aver -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION g_rotacf calculates the rotational correlation function…
NAME g_rotacf – calculates the rotational correlation function for molecules VERSION 4.0.1 SYNOPSIS g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]d -[no]aver -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION g_rotacf calculates the rotational correlation function…
NAME g_rmsf – calculates atomic fluctuations VERSION 4.0.1 SYNOPSIS g_rmsf -f traj.xtc -s topol.tpr -n index.ndx -q eiwit.pdb -oq bfac.pdb -ox xaver.pdb -o rmsf.xvg -od rmsdev.xvg -oc correl.xvg -dir rmsf.log -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]res -[no]aniso -[no]fit DESCRIPTION g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard…
NAME g_rmsf – calculates atomic fluctuations VERSION 4.0.1 SYNOPSIS g_rmsf -f traj.xtc -s topol.tpr -n index.ndx -q eiwit.pdb -oq bfac.pdb -ox xaver.pdb -o rmsf.xvg -od rmsdev.xvg -oc correl.xvg -dir rmsf.log -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]res -[no]aniso -[no]fit DESCRIPTION g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard…
NAME g_rmsdist – calculates atom pair distances averaged with power 2, -3 or -6 VERSION 4.0.1 SYNOPSIS g_rmsdist -f traj.xtc -s topol.tpr -n index.ndx -equiv equiv.dat -o distrmsd.xvg -rms rmsdist.xpm -scl rmsscale.xpm -mean rmsmean.xpm -nmr3 nmr3.xpm -nmr6 nmr6.xpm -noe noe.dat -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -nlevels int -max real…
NAME g_rmsdist – calculates atom pair distances averaged with power 2, -3 or -6 VERSION 4.0.1 SYNOPSIS g_rmsdist -f traj.xtc -s topol.tpr -n index.ndx -equiv equiv.dat -o distrmsd.xvg -rms rmsdist.xpm -scl rmsscale.xpm -mean rmsmean.xpm -nmr3 nmr3.xpm -nmr6 nmr6.xpm -noe noe.dat -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -nlevels int -max real…
NAME g_rms – calculates rmsd’s with a reference structure and rmsd matrices VERSION 4.0.1 SYNOPSIS g_rms -s topol.tpr -f traj.xtc -f2 traj.xtc -n index.ndx -o rmsd.xvg -mir rmsdmir.xvg -a avgrp.xvg -dist rmsd-dist.xvg -m rmsd.xpm -bin rmsd.dat -bm bond.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -what enum -[no]pbc -fit…
NAME g_rms – calculates rmsd’s with a reference structure and rmsd matrices VERSION 4.0.1 SYNOPSIS g_rms -s topol.tpr -f traj.xtc -f2 traj.xtc -n index.ndx -o rmsd.xvg -mir rmsdmir.xvg -a avgrp.xvg -dist rmsd-dist.xvg -m rmsd.xpm -bin rmsd.dat -bm bond.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -what enum -[no]pbc -fit…
NAME g_rdf – calculates radial distribution functions VERSION 4.0.1 SYNOPSIS g_rdf -f traj.xtc -s topol.tpr -n index.ndx -o rdf.xvg -sq sq.xvg -cn rdf_cn.xvg -hq hq.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -bin real -[no]com -rdf enum -[no]pbc -[no]norm -[no]xy -cut real -ng int -fade real -nlevel int -startq real -endq…