[gmx-users] Clustering

[Erik Marklund]

Hi,

It's been a while since I used g_clustsize, but if I'm not mistaken you get the number of molecules per cluster as output, from which you can estimate the physical size of the clusters with a few assumptions. If that's not good enough you also get the identities of the molecules in the clusters, which you can then use as input, along with the trajectory, for g_gyrate (or similar) to get more information.

trjconv -cluster doesn't calculate the sizes or report anything new, so I find it mostly useful for visualization in this context.

Best,

Erik


15 apr 2012 kl. 12.02 skrev dina dusti:

> Dear Erik,
> 
> Thank you very much from your response, but I want to calculate the radius of these cluster. I want to know that I should do clustering with trjconv -cluster similar with micelle clustering and then calculate the radius of these?
> 
> Best Regards
> Dina
> 
> From: Erik Marklund <erikm at xray.bmc.uu.se>
> To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
> Sent: Sunday, April 15, 2012 12:58 PM
> Subject: Re: [gmx-users] Clustering
> 
> Try g_clustsize
> 
> Erik
> 
> 15 apr 2012 kl. 09.00 skrev dina dusti:
> 
>> Dear GROMACS Specialists,
>> 
>> May I know about clustering, Please?
>> I want cluster small organic molecules. Is it possible? They collected in some places together and they are separate in the other place.
>> Please help me.
>> 
>> Thank you very much in advance.
>> Best Regards
>> Dina
>> 
>> 
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> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
> 
> 
> 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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