[gmx-users] g_clustsize

[Ran Friedman]

Vitaly Chaban wrote:
> Hi Ran,
>
> I will try your advice. And for what purpose should '-mol' be used?
>   
To cluster molecules.
In this case, you topology is read from the .tpr file and all of the
molecules there are taken into account for clustering.
> Vitaly
>
>
> RF> Hi,
> RF> Use -n without -mol. Clustering will be atom based.
>
> RF> Good luck,
> RF> Ran.
>
> RF> Vitaly Chaban wrote:
>   
>>> 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
>>>
>>> Why does it not 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
>>>
>>>       
>
>
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