[gmx-users] ED analysis: help on cosine content and overlap of the fluctuations

Alan Dodd anoddlad at yahoo.com
Fri Apr 13 13:06:29 CEST 2007

Short answer? RMSD is a lousy measure of convergence :)

----- Original Message ----
From: Caterina Arcangeli <caterina.arcangeli at casaccia.enea.it>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, April 13, 2007 10:58:54 AM
Subject: [gmx-users] ED analysis: help on cosine content and overlap of the fluctuations

Dear all,

I performed essential dynamics (ED) analysis on my protein (253 amino
acids). The simulation (10ns) achieves stability in the RMSD after
6.0ns, but a convergence analysis based on cluster analysis (as
described by Daura, 1999) indicates that the conformational sampling
reaches a stable value only for the last 1.0ns.

So, I've performed ED on both 6-10 ns (M1) and 9-10ns (M2) time interval
using g_covar.

To check if the principal modes are well defined, I've calulated the
ovelap of the sampling between the first and second half of the
trajectories (I've splitted M1 and M2 into two halves) and the cosine
content of the first eigenvectors:
- the normalized overlaps are 0.499 (M1) and 0.434 (M2);
- the subspace overlaps (rmsip) for the first 10 eigenvectors are 0.748
(M1) and 0.686 (M2);
- the cosine content of the first eigenvectors is 0.828 (pc1) for M1 and
0.125 (pc1) for M2.

So, apparently, the two method are inconsistent:
a higher rmsip value is observed for M1 (according to Amadei, a rmsip
value > 0.7 shows a reasonable convergence) wheras the lower cosine
content is obtained for M2 (according to Hess, a value < 0.5 indicates
jumping between clusters and not a merely random diffusion).

My questions are: which time window better describe the dynamics of my
protein? From where come out this inconsistency? What I'm wrong?
Thank to all.


P.S. I aware that 10 ns are in general insufficient to describe the
thermodynamics of a protein but I want just to have an idea of some
structural properties of my protein.

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