Thank you so much! The sieve keyword worked.
Sent from my iPhone
On Sep 27, 2012, at 10:29 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Sep 27, 2012 at 9:08 PM, Kira Armacost
> <kza0004.tigermail.auburn.edu> wrote:
>> Size (60000) of SymmetricMatrix is too big. Please limit the size to be less than 32768.
>> The first pass through the trajectory is complete.
>
> Mea culpa - I was totally unaware of this size limit.
>
> I have 3 suggestions:
>
> 1) Use the 'sieve' keyword, something like 'sieve 5' or 'sieve 10' -
> this will cut down on the initial matrix size.
>
> 2) Try clustering with cpptraj; there is no sieve keyword but also no
> size limit (other than available memory). This may take a while though
> and cpptraj only uses a hierarchical agglomerative algorithm.
>
> 3) Remove the size limitation from ptraj - just comment out lines
> 5428-5431 of clusterLib.c and recompile. However I can't vouch for the
> behavior after this; it's not my code and I'm not sure if the size
> limitations are there for a specific reason.
>
> Good luck,
>
> -Dan
>
>>
>> I used a .binpos file.
>>
>> Kira
>>
>> ________________________________________
>> From: Daniel Roe [daniel.r.roe.gmail.com]
>> Sent: Thursday, September 27, 2012 3:39 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Large trajectory for cluster analysis in ptraj
>>
>> Hi,
>>
>> On Thu, Sep 27, 2012 at 2:33 PM, Kira Armacost
>> <kza0004.tigermail.auburn.edu> wrote:
>>> I was reading somewhere about it. It originally failed me with 60,000
>>> frames, so I reduced the size of it after reading it only accepted 32,000
>>> frames. I could be wrong, but I couldn't get it to work with 60,000
>>> frames.
>>
>> What version of AmberTools are you using? How exactly did the
>> calculation fail (segmentation fault etc)? Did it fail immediately or
>> was it after some calculation had occurred? Also, do you happen to
>> have the exact output given to you by ptraj available? If so, please
>> send it to me off-list. I have run clustering for similar-length
>> trajectories and have not run into any issues, so it may be you have
>> run into a bug in the version of ptraj you are using.
>>
>> -Dan
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Sep 29 2012 - 15:00:03 PDT
