[gmx-users] Re: RE : essential dynamics

[Tsjerk Wassenaar]

Hi Bharat,

On Tue, Feb 1, 2011 at 8:33 AM, bharat gupta <bharat.85.monu at gmail.com> wrote:
> Hi,
> After searching though gmxuserlist I found the relevant thread for ED... I
> followed the following steps :-

What thread are you referring to?

> 1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha
> atoms only)
> 2) g_anaeig - to generate eigen vectors

g_covar calculates the eigenvectors. It's what you end up with through
diagonalization.

> 3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an error at
> this step that -

g_rmsf is not for calculating RMSD, and hasn't got much to do with
eigenvector analysis. That's what g_anaeig is for (like with the
option -rmsf). Using g_anaeig will avoid the error you observe.

As a side note, 3 ns is rather short for this sort of thing. You have
to check the cosine content of the first principal components to see
if you've reached equilibrium already.

Cheers,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands