[gmx-users] g_clustsize

[Justin Lemkul]

On 7/19/12 8:06 AM, mohammad agha wrote:
>
>
>
>
> 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

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