[gmx-users] Clustering

[dina dusti]

Hi Erik,

Thank you very much from your response.

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: Monday, April 16, 2012 12:07 PM
Subject: Re: [gmx-users] Clustering
 

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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