[gmx-users] Regarding gromos method in g_cluster

[bipin singh]

Now got the point. Thank you Tsjerk Sir and Prof. David for the help.


On Wed, Jul 31, 2013 at 1:42 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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.
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-- 
*-----------------------
Thanks and Regards,
Bipin Singh*