[gmx-users] Problem with gmx clustsize ..(Not enough memory. Failed to calloc)

[Mark Abraham]

Hi,

Clustering requires that you build a matrix in memory that contains the
difference between each structure you intend to cluster. If you e.g. use
every frame from your trajectory, then you will typically exhaust the
available memory, as here. Reconsider how you will find out the period
between statistically independent observations, and (if needed once you
have done the former) access a node with more memory.

Mark

On Sat, May 12, 2018 at 4:18 PM Sergio Garay <sergio.alberto.garay at gmail.com>
wrote:

> Dear Gromacs users
>
> I am trying to analyse a MD simulation of 30 lipopeptides in water, in
> particular I would like to obtain the average number of these molecules in
> each assembly, along the time. I have tried g_clustsize with my simulation
> box with only the lipopeptides. For that I prepared a tpr file for these
> molecules only. But I have these error:
>
> *g_clustsize -f 0-100ns.xtc -s micelle-alone.tpr -nc -mol -dt 1000*
>
> Fatal error:
> Not enough memory. Failed to calloc -1082130432 elements of size 4 for
> grps[j].nm_ind
> (called from file
> /home/sgaray/Programas/gromacs-5.0.4/src/gromacs/fileio/tpxio.c,
> line 2510)
>
> Could someone tell me what I am doing wrong?
>
> Thank you in advance.
>
>
> --
>
>
>
>
>
>
>
>
> *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs.
> BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 -
> Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54
> (342) 4575-221 *
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