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

Carsten Kutzner ckutzne at gwdg.de
Tue Aug 1 17:46:25 CEST 2006

> PAUL NEWMAN wrote:
>  > 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?
>  >Carsten
> 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?

Hi Paul,

with a box size of 400nm^3 and a standard fourierspacing (= maximum distance
between the pme grid points) of 0.12 nm you end up with a pme grid of
3334^3 points which is HUGE, so you run out of memory. (A typical pme grid for
a 100000 atom water system will have around 100^3 pme grid points.)

If you do not need periodic boundary conditions (?) you could switch them off and
also pme and then explicitly calculate all coulomb interactions, which should be
fast with 100 atoms. I think you have to set rlist=nstlist=0 for explicit coulomb


>  I can send you all my files if you want. Any suggestion  would be  
> highly  appreciated and thanks in advance.
> Cheers,    
> Paul
> National Tsing Hua University (ÇåÈA´óŒW)
> ÖxÖxÄãµÄŽÍæ
> I appreciate your help. Thanks!
> Os agradezco la ayuda. Gracias!
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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