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

[Bert de Groot]

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.

cheers

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________