g_clustsize(1) [debian man page]
g_clustsize(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_clustsize(1) NAME
g_clustsize - calculate size distributions of atomic clusters VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_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 -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -cut real -[no]mol -[no]pbc -nskip int -nlevels int -ndf int -rgblo vector -rgbhi vector DESCRIPTION
This program computes the size distributions of molecular/atomic clusters in the gas phase. The output is given in the form of an .xpm file. The total number of clusters is written to an .xvg file. When the -mol option is given clusters will be made out of molecules rather than atoms, which allows clustering of large molecules. In this case an index file would still contain atom numbers or your calculation will die with a SEGV. When velocities are present in your trajectory, the temperature of the largest cluster will be printed in a separate .xvg file assuming that the particles are free to move. If you are using constraints, please correct the temperature. For instance water simulated with SHAKE or SETTLE will yield a temperature that is 1.5 times too low. You can compensate for this with the -ndf option. Remember to take the removal of center of mass motion into account. The -mc option will produce an index file containing the atom numbers of the largest cluster. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input, Opt. Portable xdr run input file -n index.ndx Input, Opt. Index file -o csize.xpm Output X PixMap compatible matrix file -ow csizew.xpm Output X PixMap compatible matrix file -nc nclust.xvg Output xvgr/xmgr file -mc maxclust.xvg Output xvgr/xmgr file -ac avclust.xvg Output xvgr/xmgr file -hc histo-clust.xvg Output xvgr/xmgr file -temp temp.xvg Output, Opt. xvgr/xmgr file -mcn maxclust.ndx Output, Opt. Index 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 -cut real 0.35 Largest distance (nm) to be considered in a cluster -[no]molno Cluster molecules rather than atoms (needs .tpr file) -[no]pbcyes Use periodic boundary conditions -nskip int 0 Number of frames to skip between writing -nlevels int 20 Number of levels of grey in .xpm output -ndf int -1 Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used. -rgblo vector 1 1 0 RGB values for the color of the lowest occupied cluster size -rgbhi vector 0 0 1 RGB values for the color of the highest occupied cluster size SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_clustsize(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)