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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_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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