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)