Thank you for the reply. Since I am doing this for the first time, I wanted
to know if I am supposed to create 3 separate inputs to run in cpptraj to
do the methodology you suggested.
Regards,
Sruthi
On Tue, 1 Jun 2021 at 6:33 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You are likely running out of memory. This is why your problems during
> clustering went away when you reduced the number of input frames by a
> factor of 5. The solution is to do everything on disk. So instead of
> loading all coordinates into memory, separate the principal component
> analysis into three separate phases:
>
> 1) Create average coordinates.
> 2) Rms fit your trajectory to average coordinates, calculate the
> covariance matrix, write out the fit trajectory, diagonalize the
> matrix and write out the "modes" data (i.e. eigenvectors and
> eigenvalues).
> 3) Read in the "modes" data, calculate principal component projections
> from the fit trajectory, do the Kullback-Leibler divergence analysis.
>
> This way, the most memory you need is to store the covariance matrix,
> modes, and other data of that type. Hope this helps,
>
> -Dan
>
> PS - Note that there appears to be a small error in the input you
> posted (in pca.in). The 'nmwiz' keyword should be part of the
> diagmatrix command, not on a separate line.
>
>
> On Mon, May 31, 2021 at 1:22 PM Sruthi Sudhakar
> <sruthisudhakarraji.gmail.com> wrote:
> >
> > Dear all,
> >
> > I have been doing pca analysis on an accelerated MD trajectory of 500ns
> > (250,000 frames). I have attached the input file I have used for the
> study.
> > The job stops at the createcrd stage. Basically, the job gets killed at
> > 30%. The same happened during the cluster analysis reading every frames.
> > The clustering error was solved when I changed the input to read every
> 5th
> > frame. Now since this is repeating in pca analysis, kindly help regarding
> > the same.
> >
> >
> > Regards,
> > Sruthi Sudhakar
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Received on Tue Jun 01 2021 - 07:00:01 PDT
