Re: [AMBER] Cpptraj: std::bad_alloc error

From: Daniel Roe <>
Date: Wed, 9 Jan 2019 09:48:05 -0500

Hi there,

On Wed, Jan 9, 2019 at 6:34 AM Nikolay N. Kuzmich <> wrote:
> The amount of memory should be sufficient.
> Could you please tell me what is the possible source of trouble here?

A 2D RMS plot in CPPTRAJ is stored as an upper-triangle matrix, the
size of which is (Nframes*(Nframes-1))/2. Since you have 800000
frames, this translates to 319999600000 elements, which requires about
1.2 TB to store in single-precision floating point representation (I
should probably add output of an estimate for the size to the 2drms

I'm currently working on adding disk-cached data sets to CPPTRAJ, but
it's not ready for prime time. Your best bet in this case is to make
one or more 2D RMS plots, choosing different subsets of frames. Using
every 10th frame will require about 12 GB, which may be more feasible
for you. Hope this helps,


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Received on Wed Jan 09 2019 - 07:00:02 PST
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