Jiyanyin
Thanks very much.
Rami
On 4/26/11 12:58 PM, "Jianyin Shao" <jyshao2004.gmail.com> wrote:
> 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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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 - 10:30:02 PDT
