> The syntax for verbose is "verbose" followed by an integer. The purpose is
> to let the developer check some internal information during the clustering.
> Using "verbose" option may generate excessive output and cause confusion,
> thus not advised.
>
Thanks for the info. Would mind telling me what integer is commonly used?
I'm curious.
>
>
> Readmerge does not require the file PairwiseDistances to be present. It
> will calculate the (rms-fitted) distances between frames, but will not try
> to rewrite a new PairwiseDistance file.
>
Do you Readmerge will not overwrite PairwiseDistance file if it's ready
present in the current folder?
> I don't know how to estimate the memory usage in Perl. The memory
> management in Perl is mostly automatic, that is why I feel it is easy to
> write a script. Maybe someone else can help me with that. I will let you
> know when the silhouette function is fully incorporated in the ptraj.
>
Ok, just FYI. I ran it on a new machine and it turned out using more than
10.5GB ram. I have another larger system that ended up using 18GB ram with
this perl script.
Thanks,
Dong Xu
>
>
> On Fri, Jul 4, 2008 at 1:21 PM, Dong Xu <d1xu.ucsd.edu> wrote:
>
>> Hi Jianyin,
>>
>> The silhouette.pl script froze my computer with 4GB ram when I ran it on a
>> 570MB PairwiseDistances and 12140 frames in ClusterMerging.txt. I wonder if
>> there's a way to estimate the memory usage and run time based on the input
>> filesize? Do you have any silhouette programs that are binaries compiled in
>> C or Fortran?
>>
>> Thanks,
>>
>> Dong
>>
>>
>> On Thu, Jul 3, 2008 at 11:33 PM, Dong Xu <d1xu.ucsd.edu> wrote:
>>
>>> Also, when you use "Readmerge" to read ClusterMerging.txt generated by
>>> averagelinkage, does PairwiseDistances file have to be present? If not, will
>>> Readmerge re-calculate PairwiseDistances?
>>>
>>> Thanks,
>>>
>>> -DX
>>>
>>>
>>> On Thu, Jul 3, 2008 at 11:28 PM, Dong Xu <d1xu.ucsd.edu> wrote:
>>>
>>>> Hi Jianyin,
>>>>
>>>> I see there's an option [verbose *verb*]. Could you tell me how to use.
>>>> The clustering manual didn't mention it at all.
>>>>
>>>> Thanks,
>>>>
>>>> -DX
>>>>
>>>>
>>>> On Fri, May 30, 2008 at 10:11 AM, Jianyin Shao <jyshao2004.gmail.com>
>>>> wrote:
>>>> >
>>>> >
>>>> >>
>>>> >> I understand that "X" labels the correspondent frames to the cluster
>>>> >> members. I wrote a python script to translate "X" to frame number.
>>>> But
>>>> >> what I wanted to know was how to obtain or extract the frame numbers
>>>> >> for the cluster representatives in "filename.rep.ci" files.
>>>> >
>>>> > One "dumb" trick you may try is to use the representative structure as
>>>> > reference and run rms fitting for the entire trajectory. The one with
>>>> rmsd
>>>> > of 0 should be the representative frame.
>>>> >>
>>>> >> Since ptraj already has "rms" command, rms fitting in clustering
>>>> seems
>>>> >> a bit redundant if "rms" command is explicitly required prior to
>>>> >> running "cluster" command.
>>>> >
>>>> > The rms command will fit to a specific structure. In clustering, the
>>>> > structures in the trajectory will be aligned to different
>>>> representative
>>>> > structures of clusters to obtain reasonable centroids.
>>>> >
>>>> >
>>>> > Good luck,
>>>> >
>>>> > Jianyin
>>>> >
>>>> >
>>>>
>>>>
>>>
>>
>
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Received on Wed Jul 09 2008 - 06:07:34 PDT
