[gmx-users] Failed to allocated u bytes of aligned memory (mdrun)

Erik Lindahl lindahl at cbr.su.se
Tue Aug 1 17:45:26 CEST 2006


> Thanks Carsten for replying so fast. In my simulation I consider a  
> single polyelectrolyte chain consisting of 50 charged beads of  
> valency -1  with 50 oppositely charged counterions of same valency  
> so my system is 100 atoms. My box simulation is 400 nm x 400 nm x  
> 400 nm  and the polyelectrolyte length is 100 nm. I'm runnig in a  
> single processor. I think my system is small, isn't it?

No, your number of atoms is small, but your simulation box is huge  
for PME. The default grid spacing is 0.12nm, which means you are  
trying to allocate a box with roughly 3400^3 = 3.9*10^10 cells.

Each cell element is a complex number, so you would need over 300  
_gigabytes_ of memory just for that PME grid.



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