[gmx-users] 'Cannot allocate memory problem' while performing g_cluster

[David]

On Sat, 2004-09-25 at 08:11, sunita at chem.iitb.ac.in wrote:
> Dear Users,
> 
> I am having following error while performing g_cluser.
> It is working fine for small time range. But problem appears for large
> time fragment e.g. 20 ns .xtc file which has only protein coordinates. I
> don't want to do it in fragments. How can I get the actual cluster over
> the whole trajectory?
> 
> 
> ==========================================================================
> Last frame      40000 time 20000.000
> Allocated 11765880 bytes for frames
> Read 20001 frames from trajectory 30ns_protein.xtc
> Computing 20001x20001 RMS deviation matrix
You need
20000^2 = 4e8 x 4 bytes = 1.6 GB RAM

IIRC the program has a skip option where you just look at every n'th
frame. Put it to 10 to start with.

> # RMSD calculations left: 0
> 
> The RMSD ranges from 0.0208186 to 0.414795 nm
> Average RMSD is 0.0419409
> Number of structures for matrix 20001
> Energy of the matrix is 1211.9 nm
> WARNING: rmsd minimum 0 is below lowest rmsd value 0.0208186
> 
> Back Off! I just backed up rmsd-dist_native.xvg to ./#rmsd-dist_native.xvg.1#
> Making list of neighbors within cutoff Fatal error: realloc for nnb[i].nb
> (8480 bytes, file g_cluster.c, line 482, nnb[i].nb=0x0x66b2cef0): Cannot
> allocate memory
> ===============================================================================
> g_cluster generated the following incomplete log file.
> 
> ==================================cluster.log==========================
> Using gromos method for clustering
> Using RMSD cutoff 0.1 nm
> The RMSD ranges from 0.0208186 to 0.414795 nm
> Average RMSD is 0.0419409
> Number of structures for matrix 20001
> Energy of the matrix is 1211.9 nm
> =======================================================================
> 
> Thanks for any suggestion.
> 
> regards,
> Sunita
> 
> 
> 
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-- 
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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