[gmx-users] Re: Normal Mode limits for memory

Berk Hess gmx3 at hotmail.com
Mon Aug 9 12:18:13 CEST 2004

>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: statk002 at fiu.edu
>CC: gmx-users at gromacs.org
>Subject: [gmx-users] Re: Normal Mode limits for memory
>Date: Sat, 7 Aug 2004 11:39:43 +0200 (CEST)
>On Fri, 6 Aug 2004 statk002 at fiu.edu wrote:
> >Hello Dr.Spoel
> >I am trying to run a NM simulkation but keep running into memory 
>allocation problems.
> >
> >The code that I input is
> >g_nmeig_d -f nm.mtx -s 1CF3_nm.tpr -o eigenvalue.xvg -v eigenvector.trr
> >
> >The error I get is :
> >Reading frame       0 time    0.000   Dimensionality of matrix: 17454
> >Fatal error: calloc for hess (nelem=304642116, elsize=8, file 
>gmx_nmeig.c, line 121): Cannot allocate memory
>You need 2.5 Gb memory for this operation. You could use a subset of your
>system (only Ca for instance).

This is not possible as Bert said.

You could try to use a single precision g_nmeig, this would require
half of the amount of memory, but it might not be accurate enough.
You can just use the double precision tpr file.
g_nmeig could be extremely slow if you have less than 1 GB of memory
in your machine.


Hotmail en Messenger on the move 

More information about the gromacs.org_gmx-users mailing list