Dan,
It's AmberTools12. Here's my output:
1% ............ 25% ............ 50% ............ 75% ............ 100% Error in AllocateSymmetricMatrix,
Size (60000) of SymmetricMatrix is too big. Please limit the size to be less than 32768.
The first pass through the trajectory is complete.
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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Received on Thu Sep 27 2012 - 20:30:02 PDT
