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: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
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