[gmx-users] Normal Mode Analysis

[David]

On Wed, 2003-03-12 at 05:17, Matthew Lardy wrote:
> Hi all,
> 
> Is there some limit of peptide size when performing normal mode analysis?
> I have been trying, unsuccessfully, to perform normal mode analysis of a
> peptide pulled from the PDB Databank.  The protein 2BBM, chain A, is about
> 150 residues.  If there is some sort of upper limit to normal mode
> analysis, what is it?  I am losing my mind of this.  :)
probably memory,
150 residues is roughly 1500 atoms, so that would give you a (3x1500)^2
matrix, or 20.25 million points, or 162 Mb. That should be fine if you
have at least 256 megabytes of memory. 

Filesize limit also seems to indicate that you have something bigger
than 2 Gb, which is 12 times what you describe above..

> 
> Thanks in advance,
> Matthew
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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