AMBER Archive (2008)

Subject: Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Tue Jul 08 2008 - 23:45:46 CDT

On 7/8/08, Dong Xu <d1xu_at_ucsd.edu> wrote:
>
>
>
>
>
>> 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.
>

You can try 6 or 7.

  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?
>

If a correct PairwiseDistances file exists in the current directory, the
Readmerge will read it. If not, Readmerge will calculate the distance on the
fly, but it will not write or overwrite a PairwiseDistances file.

>
>> 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
>
>
>>
>

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