[gmx-users] g_clustsize

[mohammad agha]

Dear Gromacs Users,

I have several questions about g_clustsize, Please help me.
I have several micelles in my system and I want to calculate: the number of monomers in micelles and cluster number and monomer number during the time of simulation, I used from this command as is follows:
g_clustsize -f clustered.xtc -s c.tpr -tu us -mol -cut 0.7 -nc nclust.xvg -ac avclust.xvg -mc maxclust.xvg
I have 150 monomer initially in my system. I selected -cut from rdf.xvg for tail-tail that 0.7 was the first minimum in this graph. 




1- the nclust.xvg file is as follows:
@    title "Number of clusters"
@    xaxis  label "Time (us)"
@    yaxis  label "N"
@TYPE xy
  0.000000e+00         104
  6.000000e+01          88
  1.200000e+02          89
  1.800000e+02          85
  2.400000e+02          79
  3.000000e+02          79
  3.600000e+02          91
  4.200000e+02          89
.  . . . . ..  . .. . .. . .. ... .

.  . ... . ..  .. .. . . .. . .. ..

.  . ... . . . . ... .............
whereas in the first step of simulation there is no cluster and it should be 0!!!


2- when I choose -tu (ps, ms, us , ... ) there is no difference among them about time either file .xvg and graphs!!!why and where is problem?
3- how should I find the number of monomers from first to end of simulation that it should be 150 in the first step.

May I ask you to help me, Please?
Thank you in advance.
Best Regards
Sara
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