Simple math of memory calculation for nmode

From: Masaki Tomimoto <masaki.stromix.com>
Date: Thu, 1 May 2003 11:26:08 -0700

Hi All,

I have a question about a simle mathematics to calculate how much memory I need. I found the following comments from Dr. Case in Amber Mailing Archive.

http://amber.ch.ic.ac.uk/archive/200201/0055.html

The second derivative matrix is a 3N x 3N matrix, although you only need
to store half of it because it is symmetric.
So, for a 5000-atom system, you would need (15000)(15000)/2 =
112,000,000 words, or 900 MBytes just to store the matrix. Depending on
how many eigenvectors you want, you would also need a large amount of
memory to store them.

My system contains about 4000 atoms. According to the above math, I should need (4000x3)x(4000x3)/2 = 144,000,000 words, or 1.15 GB. However, when I execute nmode, it says that it require almost double, 208,497,233. Even Hessian is a symmetric matrix which requires only triangle part (that denotes "/2" is the above math), nmode requires memory space which hold entire hessian matrix?

Thanks,

Masaki Tomimoto
Received on Thu May 01 2003 - 19:53:01 PDT
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