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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Received on Tue Nov 22 2011 - 02:30:03 PST
