[gmx-users] Re: RE : essential dynamics

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Feb 1 10:28:54 CET 2011

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

> 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.



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

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