g_clustsize (1) - Linux Manuals

g_clustsize: calculate size distributions of atomic clusters


g_clustsize - calculate size distributions of atomic clusters



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


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.


-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 


 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

 View output xvg, xpm, eps and pdb files

 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

 Cluster molecules rather than atoms (needs tpr file)

 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



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