Hi,
25126 frames is quite a lot - the pairwise distance matrix alone will
contain 315645375 elements, which is still tractable but as you have
seen can take a while to process. I have a few recommendations:
1) Use the 'sieve' option to reduce the number of frames you are
clustering in the first pass. I also recommend the 'random' option in
conjunction with this.
2) Use the OpenMP version of cpptraj; the pairwise calculation and
restoration of sieved frames are both OpenMP-parallelized.
3) Try a different clustering algorithm. The default hierarchical
agglomerative algorithm is decent but is by its nature slow. We've had
good success with the 'dbscan' algorithm, although you do have to play
around a bit to get good values for minpoints and epsilon (there is a
section in the manual that covers this).
Hope this helps,
-Dan
On Thu, Jun 16, 2016 at 2:17 AM, Michael Shokhen
<michael.shokhen.biu.ac.il> wrote:
> Dear AMBER experts,
>
>
> I have Amber 14 and ambertools 15.
>
> My current task is cluster analysis of inte-ratomic distance
>
> on MD simulated 25126 frames.
>
>
> I used the following command lines in the cpptraj script:
>
>
> distance endToEnd :112.OG :165.NE2
> cluster data endToEnd clusters 3 epsilon 3.0 summary summary2.dat info info2.dat
>
> Unfortunately the analysis works extremely slow.
>
> Is there any option how to modify my cpptraj script
> that will reduce the execution time?
>
> Many thanks,
> Michael
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jun 16 2016 - 08:00:02 PDT
