[gmx-users] g_clustsize

[mohammad agha]

Dear Justin,

Thank you very much from your help.
I think that I should work more on this command and will ask you next.
I don't know why does it bother me for it's .xvg and -tu !!!

Thank you very much again.
Best Regards
Sara




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.

-Justin

>
> Can you help me about this, Please?
> Best Regards
> Sara
>
>
>>
>>
>>
>>
>> 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
> comment.
>
> -Justin
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================