[gmx-users] memory problem (normal mode analysis)

[Erik Lindahl]

Try version 3.3 instead, since that includes support for sparse  
matrix memory representation.

However, 478 amino acids might take days to diagonalize. Try it with  
something smaller first just to get familiar with the minimization  
steps, etc.

Cheers,

Erik


On Jan 29, 2006, at 12:31 PM, Sridhar Acharya wrote:

>
> Hello,
> I tried to run normal mode analysis using nm integrator, for a  
> protein of 478 aminoacids.
> The program halted with the following warning. The computer has 2GB  
> of memory.
> How to calculate the memory required while performing such normal  
> mode calculations.
> What can I do to get over this problem.
> thanks in advance.
> ###################################################################### 
> #################
> Back Off! I just backed up 1cyp_WT_md.log to ./#1cyp_WT_md.log.2#
> Reading file 1cyp_WT_b4md.tpr, VERSION 3.2.1 (double precision)
> Note: tpx file_version 31, software version 40
> Non-cutoff electrostatics used, forcing full Hessian format.
> Allocating Hessian memory...
>
> -------------------------------------------------------
> Program mdrun_d, VERSION 3.3
> Source code file: smalloc.c, line: 113
>
> Fatal error:
> calloc for full_matrix (nelem=-1439657584, elsize=8, file  
> minimize.c, line 1866)
> -------------------------------------------------------
>
> "Way to Go Dude" (Beavis and Butthead)
> : Cannot allocate memory
> ###################################################################### 
> ##############
> <sridhar.vcf>
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-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214