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

[David van der Spoel]

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.
________________________________________________________________________
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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