[gmx-users] COsine content of ED analysis

Chng Choon Peng cpchng at bii.a-star.edu.sg
Tue Sep 7 02:31:12 CEST 2004

Hi Ram,
  When you mean you've done an ED analysis, I take it as you've gotten the
eigenvalues and eigenvectors from a covariance matrix (ie after running
Then, you can use g_anaeig to get the principal components and then
"g_analyze -f proj.xvg -cc" to compute the cosine content.

A question for all:
Actually, I'm simulating a very small protein to 5-10ns and the cosine
content is still high when I use the average structure in the covariance
matrix rather than the initial structure.
So, I wonder if we really need long runs even for small proteins (< 100
residues) in order for the protein to end up in a potential well rather than

Mr. Choon-Peng CHNG
Research Associate
Computational Biology Group
BioInformatics Institute, BMSI, A*STAR
30 Biopolis Street
#07-01 Matrix Building
Singapore 138671
Tel (O): +65 64788301 Fax (O): +65 64789047

On 9/7/04 3:04 AM, "Sekar Ramachandran" <sram18 at yahoo.com> wrote:

> HI,
> I have just done an ED analysis on a 5 ns simulation.
> I would like to know the parameters and files to be
> used with g_analyze to calculate the cosine content.
> Thanks a lot for nay suggestions.
> Sincerely
> Ram
> =====
> Sekar Ramachandran
> Research Associate
> 316 Baker Laboratories
> DEpartment of Chemistry and Chemical Biology
> Cornell University
> Ithaca 14853
> phone:607-254-6767
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