[gmx-developers] Clusterizing a long-time trajectories

[David van der Spoel]

Den 2018-08-25 kl. 17:07, skrev Boris Timofeev:
> Dear David!
> thank you for your letter,
> could you give me some references of incremental clustering algorithm to 
> start with?
> Thank you in advance,
> sincerely yours,
> Boris Timofeev
A search on the www finds e.g. this
http://www.cs.fsu.edu/~ackerman/CIS5930/notes/Incremental%20clustering.pdf
> 
> 
> 
>     Воскресенье, 5 августа 2018, 23:46 +03:00 от David van der Spoel
>     <spoel at xray.bmc.uu.se>:
> 
>     Den 2018-08-04 kl. 23:00, skrev Boris Timofeev:
>      > Dear David!
>      >
>      > Option  -dr, it is new?
>      > Perhaps, you meant - dt? There is no wish to thin out a trajectory.
>     -dt indeed. The reason for long simulations is typically that
>     transitions are slow and that it take long time to equilibrate. That
>     also means that frames near each other are highly correlated and
>     therefore the -dt option is no problem. However, this is obviously
>     problem dependent.
> 
>     It could be possible to devise some kind of incremental clustering
>     algorithm that stores cluster centers and dynamically updates them. In
>     that manner the whole trajectory does not need to be stored. However
>     that would be a research project in itself, and I guess this kind of
>     algorithms has been developed long time ago. If you find such an
>     algorithm you could consider implementing it. Alternatively, if you see
>     a way of getting around the N^2 RMSD matrix in the existing algorithms
>     that would be interesting too.
> 
>      > Sincerely,
>      > Boris.
>      >
>      >
>      > Суббота, 4 августа 2018, 16:09 +03:00 от David van der Spoel
>      > <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>:
>      >
>      > Den 2018-07-26 kl. 14:02, skrev Boris Timofeev:
>      > > Dear developers!
>      > >
>      > > The existing realization of "gmx cluster" for calculations uses
>      > > RMSD-matrix,
>      > > quadratically increasing with increase in length of a trajectory,
>      > > and already since 20000 frames calculation of clusters becomes
>      > impossible
>      > > because of requirements to memory and time.
>      > >
>      > > Whether there are some special methods for a clustering of
>      > trajectories
>      > > of big duration,
>      > > containing 100000 and more frames?
>      > Use the -dr flag.
>      > >
>      > > Best wishes
>      > > Boris Timofeev.
>      > >
>      > >
>      > >
>      > >
>      > >
>      >
>      >
>      > --
>      > David van der Spoel, Ph.D., Professor of Biology
>      > Head of Department, Cell & Molecular Biology, Uppsala University.
>      > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>      > http://www.icm.uu.se
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>      >
>      > --
>      > Boris Timofeev
>      >
>      >
> 
> 
>     -- 
>     David van der Spoel, Ph.D., Professor of Biology
>     Head of Department, Cell & Molecular Biology, Uppsala University.
>     Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>     http://www.icm.uu.se
>     -- 
>     Gromacs Developers mailing list
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> 
> 
> 
> -- 
> Boris Timofeev
> 
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se