I was reading somewhere about it. It originally failed me with 60,000
frames, so I reduced the size of it after reading it only accepted 32,000
frames. I could be wrong, but I couldn't get it to work with 60,000
frames. I'm running it through a supercomputer center, and am allowed up
to 120gb memory for jobs.
On 9/27/12 3:25 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>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 - 14:00:02 PDT
