AMBER Archive (2003)

Subject: Simple math of memory calculation for nmode

From: Masaki Tomimoto (masaki_at_stromix.com)
Date: Thu May 01 2003 - 13:26:08 CDT

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://structbio.vanderbilt.edu/archives/amber-archive/2002/0056.phtml

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