[gmx-users] g_cluster analysis for structure refirement

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jul 25 10:56:43 CEST 2014

Hi James,

The first part is just conformational clustering, for which you can use
g_cluster. The easiest is then to collect the structures belonging to the
different clusters in different files (which g_cluster can do), which you
process separately to extract those properties you're interested in. Then
you can easily plot the selected properties per cluster.

Hope it helps,


On Fri, Jul 25, 2014 at 9:53 AM, James Starlight <jmsstarlight at gmail.com>

> Dear Gromacs users!
> I'd like to use g_cluster utility to cluster a big set of models produced
> by Modeller as the result of the refirement of some parts of my protein. In
> this case all structures differs only in the conformation of 1 longest loop
> (~ 30 amino acids including 2 disulphide bridges) so I need to cluster all
> models based on the RMSD in this region.   As the result I'd like to obtain
> projection of all set of conformers onto the plane of some coordinates
>  correspond to some selected structural criteriums (for instance percent of
> the occurence of secondary structure elements  in the refined (loop)
> region; and/or some geometrical criteriums like distance between pair of
> residues, occurence of the salt-bridges in this region etc. As the result
> I'd like to visualize data and chose most representative structures from
> each cluster for further MD simulation. Could such processing be performed
> by g_cluster taking into account that I have gromacs-like trr consisted of
> my conformers ? On what cluster algoritms and parameters  should I pay a
> lot of attention?
> Many thanks for suggestion,
> James
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Tsjerk A. Wassenaar, Ph.D.

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