[gmx-users] g_clustsize

[mohammad agha]

Dear Prof. Spoel

Thank you very much for your reply, but I don't understand what I want!
In the g_clustsize there is only " -cut = Largest distance (nm) to be considered in a cluster " between my questions and I don't know the base of selection for -cut. I practice different numbers for -cut and took different results but may I know the most exact number for it? 


Best Regards
Sara


________________________________
 From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, November 26, 2011 10:09 PM
Subject: Re: [gmx-users] g_clustsize
 
On 2011-11-26 18:55, mohammad agha wrote:
> Dear Prof.
>
> I have some problems about g_clustsize program and I didn't find my
> answer in mailing list. Please help me.
> I don't know what is the base of selection for -cut option?
> In my system after doing g_clustsize, when I see nclust.xvg file, it
> looks like all the atoms in the system were used to find clusters.
>
that's correct, g_clustsize -h explains it.

> @ title "Number of clusters"
> @ xaxis label "Time (ps)"
> @ yaxis label "N"
> @TYPE xy
> 0.000000e+00 413
> 1.500000e+02 362
> 3.000000e+02 348
> 4.500000e+02 304
> 6.000000e+02 274
> 7.500000e+02 255
> 9.000000e+02 243
> 1.050000e+03 233
> 1.200000e+03 218
> 1.350000e+03 211
> 1.500000e+03 199
> 1.650000e+03 190
> 1.800000e+03 192
> 1.950000e+03 179
> 2.100000e+03 172
> 2.250000e+03 170
> .....
> .....
> .....
> 5.992500e+05 9
> 5.994000e+05 10
> 5.995500e+05 9
> 5.997000e+05 9
> 5.998500e+05 9
> 6.000000e+05 9
> My system consist of 500 monmer.
>
> Please help me.
>
> Best Regards
> SARA
>
>
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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