Hi Alex,
I see. Thanks a lot for your suggestion!
I am also curious whether or not the maximum size of PairwiseDistances is
2Gb? Would the clustering analysis be faster if the file size
of PairwiseDistances can be allocated lager?
Thanks!
Junjun
On Tue, Nov 22, 2011 at 9:08 PM, Alex Rodriguez <alexdepremia.gmail.com>wrote:
> Hi!
>
> I have never employed ptraj clustering facilities but, in general,
> clustering algorithms scale with the square of the number of elements
> involved. Try to do it with a lower number of snapshots, may be not using
> all the snaps of your trajectory but, let's say, only one each five... I'm
> afraid that if you employ all of them, it would take really long...
>
> Alex.
>
>
>
> On Tue, Nov 22, 2011 at 11:07 AM, liu junjun <ljjlp03.gmail.com> wrote:
>
> > Dear All,
> >
> > I have a MD trajectory consisting of ~22,000 snapshots for a small
> peptide,
> > which has only 537 atoms. I am trying to do clustering analysis by ptraj.
> > But the clustering calculation has been running for more than 24 hours
> > without completion. This is very wired because the clustering analysis in
> > ptraj is much much faster on relatively small trajectory.
> >
> > ------------------ Some information that may needed for diagnose the
> > problem ----------------------
> > ptraj version: from AmberTools 1.5, all patch have
> been
> > applied
> > the clustering command: cluster out testcluster representative pdb
> > average pdb averagelinkage clusters 5 rms .CA
> >
> > ------------------ test of a clustering analysis on a trajectory
> consisting
> > of 1881 snapshots -------------------------
> > the calculation time: 1.5 minutes
> > file size of PairwiseDistances: 14Mb
> > the last line of ClusterMerging.txt: -1877: -1735 -1875 7.723636 1.881472
> > 2697.106445
> >
> > ------------------ clustering analysis on the trajectory consisting of
> > ~22,000 snapshots -----------------------------
> > the calculation time: more than 24 hours and not finished yet
> > file size of PairwiseDistances: 2.0Gb
> > the last line of ClusterMerging.txt: -3930: 12251 -1653 1.057229
> > 352.6313
> >
> >
> > Any helps are highly appreciated!
> >
> > Junjun
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> >
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Received on Tue Nov 22 2011 - 06:00:04 PST
