g_mindist(1) [debian man page]
g_mindist(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_mindist(1) NAME
g_mindist - calculates the minimum distance between two groups VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_mindist -f traj.xtc -s topol.tpr -n index.ndx -od mindist.xvg -on numcont.xvg -o atm-pair.out -ox mindist.xtc -or mindistres.xvg -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -[no]matrix -[no]max -d real -[no]group -[no]pi -[no]split -ng int -[no]pbc -[no]respertime -[no]printresname DESCRIPTION
g_mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are written to two separate output files. With the -group option a contact of an atom in other group with multiple atoms in the first group is counted as one contact instead of as multiple con- tacts. With -or, minimum distances to each residue in the first group are determined and plotted as a function of residue number. With option -pi the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein has seen its periodic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts. It also plots the maximum distance within the group and the lengths of the three box vectors. Other programs that calculate distances are g_dist and g_bond. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -od mindist.xvg Output xvgr/xmgr file -on numcont.xvg Output, Opt. xvgr/xmgr file -o atm-pair.out Output, Opt. Generic output file -ox mindist.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb -or mindistres.xvg Output, Opt. xvgr/xmgr file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]matrixno Calculate half a matrix of group-group distances -[no]maxno Calculate *maximum* distance instead of minimum -d real 0.6 Distance for contacts -[no]groupno Count contacts with multiple atoms in the first group as one -[no]pino Calculate minimum distance with periodic images -[no]splitno Split graph where time is zero -ng int 1 Number of secondary groups to compute distance to a central group -[no]pbcyes Take periodic boundary conditions into account -[no]respertimeno When writing per-residue distances, write distance for each time point -[no]printresnameno Write residue names SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_mindist(1)
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g_traj(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_traj(1) NAME
g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_traj -f traj.xtc -s topol.tpr -n index.ndx -ox coord.xvg -oxt coord.xtc -ov veloc.xvg -of force.xvg -ob box.xvg -ot temp.xvg -ekt ektrans.xvg -ekr ekrot.xvg -vd veldist.xvg -cv veloc.pdb -cf force.pdb -av all_veloc.xvg -af all_force.xvg -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -[no]com -[no]pbc -[no]mol -[no]nojump -[no]x -[no]y -[no]z -ng int -[no]len -[no]fp -bin real -ctime real -scale real DESCRIPTION
g_traj plots coordinates, velocities, forces and/or the box. With -com the coordinates, velocities and forces are calculated for the center of mass of each group. When -mol is set, the numbers in the index file are interpreted as molecule numbers and the same procedure as with -com is used for each molecule. Option -ot plots the temperature of each group, provided velocities are present in the trajectory file. No corrections are made for con- strained degrees of freedom! This implies -com. Options -ekt and -ekr plot the translational and rotational kinetic energy of each group, provided velocities are present in the trajec- tory file. This implies -com. Options -cv and -cf write the average velocities and average forces as temperature factors to a .pdb file with the average coordinates or the coordinates at -ctime. The temperature factors are scaled such that the maximum is 10. The scaling can be changed with the option -scale. To get the velocities or forces of one frame set both -b and -e to the time of desired frame. When averaging over frames you might need to use the -nojump option to obtain the correct average coordinates. If you select either of these option the average force and velocity for each atom are written to an .xvg file as well (specified with -av or -af). Option -vd computes a velocity distribution, i.e. the norm of the vector is plotted. In addition in the same graph the kinetic energy dis- tribution is given. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -ox coord.xvg Output, Opt. xvgr/xmgr file -oxt coord.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -ov veloc.xvg Output, Opt. xvgr/xmgr file -of force.xvg Output, Opt. xvgr/xmgr file -ob box.xvg Output, Opt. xvgr/xmgr file -ot temp.xvg Output, Opt. xvgr/xmgr file -ekt ektrans.xvg Output, Opt. xvgr/xmgr file -ekr ekrot.xvg Output, Opt. xvgr/xmgr file -vd veldist.xvg Output, Opt. xvgr/xmgr file -cv veloc.pdb Output, Opt. Protein data bank file -cf force.pdb Output, Opt. Protein data bank file -av all_veloc.xvg Output, Opt. xvgr/xmgr file -af all_force.xvg Output, Opt. xvgr/xmgr file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]comno Plot data for the com of each group -[no]pbcyes Make molecules whole for COM -[no]molno Index contains molecule numbers iso atom numbers -[no]nojumpno Remove jumps of atoms across the box -[no]xyes Plot X-component -[no]yyes Plot Y-component -[no]zyes Plot Z-component -ng int 1 Number of groups to consider -[no]lenno Plot vector length -[no]fpno Full precision output -bin real 1 Binwidth for velocity histogram (nm/ps) -ctime real -1 Use frame at this time for x in -cv and -cf instead of the average x -scale real 0 Scale factor for .pdb output, 0 is autoscale SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_traj(1)