Hi Rami,
The ptraj tries to limit the size of the resulting cluster trajectories.
Both of the files brd41_nt_bd_2.c0 and brd41_nt_bd_2.c1 contain 8836 frames.
The remaining trajectory of cluster? was written to ***.c?.1, ***.c?.2 and
so on. So your first cluster(c0) is brd41_nt_bd_2.c0 (8836 frames) plus
brd41_nt_bd_2.c0.1 (844 frames), and second cluster(c1) is brd41_nt_bd_2.c1
(8836 frames) plus brd41_nt_bd_2.c1.1 (1484 frames).
Hope this helps.
Jianyin Shao
On Tue, Apr 26, 2011 at 9:39 AM, Roman Osman <roman.osman.mssm.edu> wrote:
> I have tried to sort a trajectory with 20,000 snapshots into two clusters.
> I
> use the following input
>
> trajin ../brd4_nt_bd_200.trj 1 20000 1
>
> cluster out brd41_nt_bd_2 representative pdb \
> average pdb means clusters 2 verbose verb \
> rms sieve 20 mass ":19-30,32-39,42,46-48,72-82,85-88,90-92,94"
>
> As you can see from the attached output: brd41_nt_bd_2.txt the two clusters
> are different 9680 members in one and 10320 in the other.
> However, cluster writes to files of equal size for the two sorted
> trajectories:
> wc brd41_nt_bd_2.c0
> 6476789 64732539 524337103 brd41_nt_bd_2.c0
> wc brd41_nt_bd_2.c1
> 6476789 64732539 524337103 brd41_nt_bd_2.c1.
> Both contain only 8836 snapshots.
> The first pass filtered trajecotires are different:
> wc brd41_nt_bd_2.c0.1
> 618653 6183147 50083831 brd41_nt_bd_2.c0.1
> With 844 members
> And
> wc brd41_nt_bd_2.c1.1
> 1087773 10871787 88062071 brd41_nt_bd_2.c1.1
> With 1484 members.
> Clearly, the sum of the two is more than 1,000, which is the number of the
> sieved sample.
> I am using AT1.5
> Thanks for your help.
> Rami
> Roman Osman
> Department of Structural and Chemical Biology
> Mount Sinai School of Medicine
> New York, NY 10029
> Tel: 212-659-8627
> Fax: 212-849-2456
> e-mail: roman.osman.mssm.edu
> http://atlas.physbio.mssm.edu/~osmanlab :
>
>
>
>
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Received on Tue Apr 26 2011 - 10:00:02 PDT
