Memory problem while performing analysis on large trajectory file

[Former user]

Hi,

I am using bio3d for performing pca, dccm calculation etc on a large trajectory file of about 38GB. I am facing severe memory problems while performing the analysis even on a system with 192GB RAM.

Sorry for the comparison, on the other hand I was able to perform Essential dynamics analysis with Prody package without any problem which also involves building covariance matrix. Has it to do with any setting in R package ?

Rakesh

[Barry Grant]

DCCM analysis etc. of a trajectory that large will likely encounter these problems with the current CRAN version of Bio3D. Indeed R itself will struggle with these size of objects as it is designed to work in interactive mode having all objects accessible in the workspace (and hence in memory).

There are ways to deal with this, and 'big data' in general that are under active development, and that we intend to implement in a future version as they mature. Unfortunately we don't have a quick fix for you beyond partitioning your trajectory into smaller segments and concentrating on C-alpha atoms for example.

[Barry Grant]

For future development