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

Bert de Groot bgroot at gwdg.de
Mon Aug 9 10:41:37 CEST 2004

David van der Spoel wrote:
> 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).

AFAIK, you cannot perform NM on a subset only. What people from the NM community often do is
to switch to a more coarse-grained desciption of the system. However, such simplified forcefields
are to my knowledge not implemented in gromacs.



Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de

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