g_clustsize(1) 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 -[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


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.


-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

 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

 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

 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