Hi,
First use the 'readdata' command to read in the matrix; I would also
use the 'name' keyword to give it a name which makes it easier to work
with. Then proceed as normal, e.g.
readdata covarmatrix.dat name MyMatrix
runanalysis diagmatrix MyMatrix ...
Also, the covariance matrix calculation in 'matrix' has been OpenMP
parallelized, so using cpptraj.OMP may speed things up for you in the
future.
Hope this helps,
-Dan
On Tue, Apr 5, 2016 at 1:52 PM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Dear all,
>
> I have a PCA analysis that crashed during the "runanalysis diagmatrix"
> apparently with a memory issue (terminate called after throwing an
> instance of 'std::bad_alloc' what(): std::bad_alloc).
>
> The covariance matrix was apparently generated and I would like to test
> if it can be used further (creating it was quite time-consuming due to
> the large number of frames). However, when I tried to restart the
> "runanalysis diagmatrix" unsing a file name for the matrix instead of a
> matrix name, cpptraj complaints that the matrix does not exist although
> the file is there and looks fine.
>
> Is it possible to read in cpptraj from a file a previously created
> matrix and use it further with diagmatrix ?
>
> Thanks for any advice
>
> Best wishes
> Vlad
>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Apr 05 2016 - 13:30:05 PDT
