[gmx-users] g_clustsize

[Ran Friedman]

Hi,
Use -n without -mol. Clustering will be atom based.

Good luck,
Ran.

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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>   


-- 
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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