jalemkul at vt.edu
Thu Jul 19 15:45:41 CEST 2012
On 7/19/12 9:42 AM, mohammad agha wrote:
> Dear Justin,
> Thank you very much from your response.
> according you said I should set -cut with less than 0.7, but this doesn't answer me!
I didn't say that, but your results are completely consistent with what I said
about how g_clustsize is working and the output it is producing.
> for 0.6:
> 0.000000e+00 115
> 6.000000e+01 107
> 1.200000e+02 114
> 1.800000e+02 105
> 2.400000e+02 100
> 3.000000e+02 96
> 3.600000e+02 103
> 4.200000e+02 111
> 4.800000e+02 99
> for 0.5
> 0.000000e+00 139
> 6.000000e+01 135
> 1.200000e+02 136
> 1.800000e+02 136
> 2.400000e+02 140
> 3.000000e+02 139
> 3.600000e+02 142
> 4.200000e+02 138
> 4.800000e+02 137
As you decrease the value of -cut, you get more and more "clusters" (which
largely contain only one molecule). I suppose if you want a count of monomers
(which is the opposite of what g_clustsize does) then you could try setting -cut
to zero, but I don't know if this will even work. The code may expect a
non-zero cutoff value.
> Can you help me about this, Please?
> Best Regards
>> 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!!!
> You've set the cutoff value to 0.7 nm, so any molecules with contacts within
> this distance will be considered clustered. Out of 150 monomers, some are
> within this distance in the starting frame. Note that with 104 clusters, the
> majority of your 150 monomers are basically in individual clusters.
>> 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?
> This is odd. The code indicates that you should be able to display whatever
> units you choose. In any case, you should determine from the trajectory what
> the interval (in ps) is and plot accordingly. Time units can always be
> manipulated after the fact with simple multiplication or division operations.
>> 3- how should I find the number of monomers from first to end of simulation that it should be 150 in the first step.
> Probably not with g_clustsize. It does exactly the opposite, but perhaps you
> can back-calculate the results using a combination of output files. It's not
> immediately clear to me how you would do that, though. Perhaps someone else can
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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