[gmx-users] Regarding gromos method in g_cluster

[Tsjerk Wassenaar]

Hi Bipin,

If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD < 0.3 nm, they'll
end up in the same cluster.

Cheers,

Tsjerk


On Wed, Jul 31, 2013 at 9:45 AM, bipin singh <bipinelmat at gmail.com> wrote:

> Thanks for the reply Prof. David. But in the output it shows that "The RMSD
> ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to
> me. So I think it should write the snapshots having RMSD greater than 0.3nm
> (cutoff) to another cluster.
>
>
> On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel
> <spoel at xray.bmc.uu.se>wrote:
>
> > On 2013-07-31 07:20, bipin singh wrote:
> >
> >> Hello All,
> >>
> >> I was trying to do clustering on my MD trajectory using gromos method
> >> under
> >> g_cluster module. I got one doubt regarding the output, as I used the
> >> cutoff of 0.3nm for RMSD calculation, I was expecting that all the
> >> snapshots which have RMSD less than or equal to 0.3nm will form the
> first
> >> cluster and the rest of snapshots will form another cluster. But the
> >> output
> >> gives a single cluster. Please let me know if I have not understood it
> >> correctly.
> >>
> >
> > It means everything is within 0.3 nm RMSD from each other. Maybe your
> > system is very stable or you did not simulate very long. You can use a
> > shorter cut-off.
> >
> >
> >> I am appending the output below:
> >>
> >> ##############################**######################
> >> Using gromos method for clustering
> >> Using RMSD cutoff 0.3 nm
> >> The RMSD ranges from 0.0602553 to 0.411066 nm
> >> Average RMSD is 0.107366
> >> Number of structures for matrix 12501
> >> Energy of the matrix is 960.075 nm
> >>
> >> Found 1 clusters
> >>
> >> Writing middle structure for each cluster to clusters.pdb
> >> Counted 0 transitions in total, max 0 between two specific clusters
> >> ##############################**########################
> >>
> >>
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> > --
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> *-----------------------
> Thanks and Regards,
> Bipin Singh*
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-- 
Tsjerk A. Wassenaar, Ph.D.