[gmx-users] fatal error

[Berk Hess]

>From: Martin Höfling <martin.hoefling at gmx.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] fatal error
>Date: Wed, 23 May 2007 13:20:42 +0200
>
>Am Mittwoch, 23. Mai 2007 schrieb Sonali:
>
> > Program g_covar, VERSION 3.3
> > Source code file: smalloc.c, line: 113
> >
> > Fatal error:
> > calloc for mat (nelem=997170084, elsize=4, file gmx_covar.c, line 219)
> > -------------------------------------------------------
> >
> > "Whatever Happened to Pong ?" (F. Black)
> >
> > : Cannot allocate memory
>
>If i read the above correct, it's trying to allocate 1G * 4 * 4 or 8
>(depending on single or double prec.)
>That's at least 16G of memory and might be to much depending on available 
>mem
>and/or architecture.
>
>Cheers
>	Martin

Your group apparently has sqrt(997170084)=31578 atoms.
You could use backbone only, or maybe protein-h.

Also one should normally use the same group for fitting and covariance.

Berk.

_________________________________________________________________
Hotmail en Messenger on the move http://www.msn.nl/services