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

PAUL NEWMAN paulclizana at gmail.com
Tue Aug 1 17:10:44 CEST 2006

> Dear all:
> I made a simulation about a polyelectrolyte with some ions, it runs ok
> when I use cut-off for both Wdv and Coulomb. However I get the following
> error when I change it to PME. I attache my mdp file . Could someone
> help me to find what it's wrong in my file?. Thanks in advance.
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.1
> Source code file: fftgrid.c, line: 75
> Fatal error:
> Failed to allocated u bytes of aligned memory.
> -------------------------------------------------------

 CARSTEN wrote:
>How big is your system (number of atoms)? Seems there is not enough
>memory to initialise the pme grid. On how many CPUs and on how many
>nodes do you run?

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?
 I can send you all my files if you want. Any suggestion  would be  highly
appreciated and thanks in advance.


National Tsing Hua University (ÇåÈA´óŒW)

I appreciate your help. Thanks!
Os agradezco la ayuda. Gracias!
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