NAME
g_clustsize - calculate size distributions of atomic clusters
VERSION 4.0.1
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 -nice int -b
time -e time -dt time -tu enum -[no]w -[no]xvgr -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 a XPM
file. The total number of clusters is written to a 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
calculcation 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
-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: ps, fs, ns, us, ms or s
-[no]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-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/>.
Thu 16 Oct 2008 g_clustsize(1)