Main Table of Contents

Wed 13 Nov 2013


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

Other options

-[no]h bool no Print help info and quit
-[no]version bool no 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]w bool no 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]mol bool no Cluster molecules rather than atoms (needs .tpr file)
-[no]pbc bool yes 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