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

David van der Spoel spoel at xray.bmc.uu.se
Sat Aug 7 11:39:43 CEST 2004

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).
>Can you please gibe nay input in this regard ?
>I dont have subscription to Gromacs user list and hence I had to mail you directly.
Please subscribe then, and continue the discussion at the list.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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