[gmx-users] g_covar & g_anaeig problems

Mark Abraham mark.abraham at anu.edu.au
Wed Sep 8 03:57:14 CEST 2010

----- Original Message -----
From: Sebastian Breuers <breuerss at uni-koeln.de>
Date: Tuesday, September 7, 2010 17:47
Subject: Re: [gmx-users] g_covar & g_anaeig problems
To: gmx-users at gromacs.org

> Hey,
> taking fewer atoms by ignoring the hydrogens is a good advice. 
> Thanks a lot.

That's just the tip of the iceberg, of course. Even as little as your C-alpha atoms might be sufficient for the purpose.

> I was wondering if a more appropriate error message could be 
> generated before the program messes around in the memory. The 
> program acts as if it could handle the system size and then 
> crashes with a Segmentation fault meaning it does not properly 
> handle its memory.

Sure, that would be nice behaviour. Unfortunately the algorithms used for diagonalization are called from another library, and GROMACS can't realistically anticipate its memory usage. Moreover, finding out from the system how much virtual memory is available and from the user whether virtual memory use is acceptable is all more work than it's worth. I have added a note in the g_covar documentation to clue the user in to how best to manage the situation.


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