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 - 09:00:02 PDT
