Hi VJ,
So far the only way to cluster a very long trajectory is to use "sieve"
option. So a smaller sieved subtrajectory will be clustered in the first
step, and then all frames will be assigned to the closest clusters defined
in the first step.
Hope it helps.
Jianyin Shao
On Mon, Nov 22, 2010 at 1:22 AM, jani vinod <genomejani.gmail.com> wrote:
> Dear all,
> I have trajectory with more than 1 lakh frames and i wish to do
> hierarchical
> clustering for same
> "
> *$AMBERHOME/exe/ptraj x.prmtop <<EOF
> trajin x.traj
> cluster out testcluster representative pdb average pdb hierarchical epsilon
> 2 rms .CA
> go*
> "
> when i run the above script i am getting following error
>
> *The first pass through the trajectory is complete.
> Error in AllocateSymmetricMatrix, Size (133592) of SymmetricMatrix is too
> big. Please limit the size to be less than 32768.*
>
> So where to put the above mentioned limit
> and is it possible to carry out clustering based on all frames if the above
> limit is given.
>
> Thanks
> VJ
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Received on Mon Nov 22 2010 - 12:00:04 PST
