[AMBER-Developers] CPPTRAJ: dpeaks clustering

From: Yinglong Miao <yinglong.miao.gmail.com>
Date: Tue, 31 May 2016 10:36:31 -0700

This may be also a question on the Users mailing list, but as I try the
cpptraj density peaks (dpeaks) clustering (which is great!), I notice the
following warning regarding seiving frames:
        Restoring sieved frames.
FIXME: Adding sieved frames not yet supported.

I'm wondering whether this will be coded in the near future. Also is there
a limit on the data size for the clustering other than memory usage? The
workstation I'm running has ~64G memory, but the program exited in the
middle of matrix calculation (crashed?) even with apparently enough memory:

    Estimated pair-wise matrix memory usage: > 16.587 GB
    Pair-wise matrix set up, 91068 frames
 0% 10% 20% 30% mkdir: cannot create directory
`cluster-dpeaks-e1-ncstep1-sieve1': File exists

Any suggestions will be appreciated,


Yinglong Miao, Ph.D.
Research Specialist I, Howard Hughes Medical Institute
Assistant Project Scientist, Department of Pharmacology
University of California, San Diego
Tel: 858-822-0255; Email: yimiao.ucsd.edu
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Received on Tue May 31 2016 - 11:00:05 PDT
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