[AMBER] Reducing memory usage in lifetime analyses

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Wed, 26 Sep 2018 06:15:29 +0000

Hello again Amber users and developers

I return with more questions. When running cpptraj hbond analyses including lifetime analysis, the memory demand for the analyses I am running sometimes peak at around 80 GB which is a bit more than I have access to. I am assuming that this is because something in the lifetime analysis is kept in memory since running just the hbond analysis lands me around 2-5% memory requirements.

So this is my question, is there any way to perform the lifetime analysis on the entire set though in some way use intermediate files and thus manage to reduce the memory requirement for the analyses?

This is the input I’m using

   hbond S1 series out series_file.out \
   donormask :URA.N1 donorhmask :URA.H1 \
   acceptormask :URA.O1 \
   avgout average_file.out nointramol
   runanalysis lifetime S1[solutehb] out lifetime_file.out

Keeping my fingers crossed!

Best regards
// Gustaf

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Received on Tue Sep 25 2018 - 23:30:02 PDT
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