Hi Dan,
Out of curiosity, never tested ptraj for systems where there are million
atoms or more, will ptraj be able to process trajectory say if you had the
memory on the processors.
Most of times I would like to analyze trajectories having 100 gb excess
data course using a submission scripts on nodes with 32 cores. Again I have
not tested it on nodes of nersc. Maybe I can compile ptraj on these
nodes.......
Thanks,
Ganesh
On Sep 27, 2012 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 - 20:30:03 PDT
