[gmx-users] Re: RE : essential dynamics

bharat gupta bharat.85.monu at gmail.com
Tue Feb 1 11:04:13 CET 2011

Thanks for the reply ...

I am following this thread -
<http://oldwww.gromacs.org/pipermail/gmx-users/2004-May/010438.html>Also I
read the following paper http://pubs.acs.org/doi/abs/10.1021/jp983120q
dynamics of GFP) in which they have carried out such projections of the
eigen vector in order to find the regions showing minimum and maximum

What I am thinking is shall I take those c-alpha atoms that are well stable
and equilibrated after referring to RMSD graph generated after simulation

I am stating here what I have done so far and what I have to analyze :-

I exchanged the loops regions of GFP with loops of longer length taken from
pdb .. I simulated both the crystal str. and modeled strs. to compare how
the loop incorporation leads to the change in the structure of GFP ....
Since the RMSD of the GFP crystal str and that of model are in comparable
range .. I thought of looking at the motions of loops in the structure that
are giving such fluctuations in RMSD of model and for that I decided to
generate eigen vectors and project them in 3d (like the one given in paper
mentioned above) to see how that particular loop behaves .. I don't know
whether what I have hypothesized is correct or not .. since I am not able to
find any other insilico method apart from MDS for such a study .. Also if my
prediction comes out to be good enough I have to carry out such insertion in
the wet lab and has to check for fluorescence ..any help in this regard will
be appreciated...

On Tue, Feb 1, 2011 at 1:28 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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
> --
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