table of contents
g_clustsize(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_clustsize(1) |
NAME¶
g_clustsize - calculate size distributions of atomic clustersSYNOPSIS¶
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 vectorDESCRIPTION¶
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.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Portable xdr run input file
Index file
X PixMap compatible matrix file
X PixMap compatible matrix file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Index file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
Time unit: fs, ps, ns, us, ms or s
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Largest distance (nm) to be considered in a cluster
Cluster molecules rather than atoms (needs .tpr file)
Use periodic boundary conditions
Number of frames to skip between writing
Number of levels of grey in .xpm output
Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used.
RGB values for the color of the lowest occupied cluster size
RGB values for the color of the highest occupied cluster size
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |