[gmx-users] g_clustsize

[Vitaly Chaban]

Hi GMX Colleagues,

I need a little clarification.

I try to calculate a distribution of clusters of ions in a system with
several cations and anions and a few solvent molecules. So I just need
a number of cluster consisting of ions and the size of the each (how many
ions the cluster includes).

To do this I use
g_clustsize(402) -n index.ndx -mol -s topol.tpr
where index.ndx contains only the number of the atoms of the ions.

but the programme outputs:
Back Off! I just backed up temp.xvg to ./#temp.xvg.1#
Reading frame       0 time    0.000   Reading file topol.tpr, VERSION 4.0.2 (single precision)
Reading file topol.tpr, VERSION 4.0.2 (single precision)
Using molecules rather than atoms. Not reading index file index.ndx

Ehat dows it now read the index file with the atom number I want to
cluster?


When I see for example histo-clust.xvg:

@    title "Cluster size distribution"
@    xaxis  label "Cluster size"
@    yaxis  label "()"
@TYPE xy
    0     0.000
    1    19.531
    2     4.583
    3     1.707
    4     0.647
    5     0.259
    6     0.060
    7     0.140
    8     0.048
    9     0.054
   10     0.020
   11     0.022
   12     0.000
................
................
................
  577    31.096
  578    33.457
  579    36.982
  580    28.942
  581    31.311
  582    34.850
  583    38.401
  584    30.307


It looks like all the atoms in the system were used to find clusters.

And maxclust.xvg:

@    title "Max cluster size"
@    xaxis  label "Time (ps)"
@    yaxis  label "#molecules"
@TYPE xy
  0.000000e+00         577
  1.000000e-01         576
  2.000000e-01         565
  3.000000e-01         550
  4.000000e-01         567
  5.000000e-01         572
  6.000000e-01         566
  7.000000e-01         578
  8.000000e-01         567
  9.000000e-01         565
  1.000000e+00         563
  1.100000e+00         579
  1.200000e+00         566



Please anybody let me know how to find clusters only among those
particles I point out in the index file. So I need only the clusters
consisting of ions but solvent is not of interest in my case.


Thank you in advance,
Vitaly



===============================
Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, mob.: +38-097-8259698