[gmx-users] g_clustsize

[Vitaly Chaban]

Hi Ran,

I will try your advice. And for what purpose should '-mol' be used?

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
>>