Hi,
On Thu, Sep 27, 2012 at 12:29 PM, Kira Armacost
<kza0004.tigermail.auburn.edu> wrote:
> I have a large trajectory (60,000 frames) and am trying to perform a cluster analysis on it. I know that ptraj only has the capability of using 32,000 frames for each analysis
Where did you come up with this limit? AFAIK ptraj should only be
limited by the size of available memory.
> , so I've done 4 cluster analyses for frames 1-15000, 15-30000, 30-45000, and 45-60000. Is this the right way to go about it?
It depends on what you are looking for. Cluster analysis of parts of a
system may or may not match each other, depending on how well
converged the simulation is. If the simulation converges within the
first 15000 frames then you might expect to get similar results from
clustering 1-15000 and 15000-30000 (but still might not since
ostensibly the system is still equilibrating during the first 15k
frames). In fact, one way to measure convergence is to cluster the
first and last halves of your simulation, then compare the resulting
clusters from those to clustering of the entire simulation.
You can compare representative structures from clusters and compare
populations to get a rough idea of the structures your system is
sampling during each time course. However, if you want to look at
overall behavior you should still cluster on all frames (which should
be possible). You can speed this process up by using the 'sieve'
keyword.
Hope this is helpful.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Sep 27 2012 - 13:30:02 PDT
