thank you for the reply
i will try and share my experience
On Tue, Nov 23, 2010 at 1:26 AM, Jianyin Shao <jyshao2004.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 23 2010 - 21:30:03 PST
