Re: AMBER: Nmode segmentation fault

From: David A. Case <>
Date: Tue, 25 Mar 2008 11:44:51 -0700

On Tue, Mar 25, 2008, James Thomas wrote:
> Test protein: 1382 atoms (successful)
> Interest protein: 5780 atoms (segmentation fault error)
> I did not do any CG minimisation before starting NR.
> I look forward to your advice on how to solve the segmentation fault problem

No real advice. You have to check how much memory you have on your system,
but nmode should report an allocation failure, not a segfault even in that
case. But the error checking for allocation failures might not be robust,
and it could be that you just have a lack of memory.

For 5780 atoms, you will need (5780*3)*(5730*3)*8 = 2.4 Gbytes of available
memory. But you haven't give much to go on: we don't know what sort of job
you are running (i.e. ntrun), the type of machine, and so on.


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Received on Fri Apr 18 2008 - 21:13:59 PDT
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