Hi,
I am running ptraj cluserting (average linkage) for MD trajectories (20 ns) of a
protein-ligand complex and
it has been running for more than 24 hours now, still not completed and the
present output at the
terminal is
.....................................................................
The first pass through the trajectory is complete.
Calculating the PairwiseDistances
Writing Pairwise Distances to file "PairwiseDistances".
Clustering using the average linkage algorithm.
I am sure people have run such cluster analysis for even longer trajectories.
Can someone
suggest me how to approach this problem to make it quicker?
will it be OK? if I split the trajectories into a few groups and do analysis
within each group?
thanks in advance,
Senthil Natesan
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Received on Fri Sep 17 2010 - 08:00:19 PDT
