[gmx-users] Normal Mode Analysis

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 10 08:21:43 CET 2011

Hi James,

> 1- Can I obtain same fluctuations along ensemble of several modes (i.e
> averaged fluctuations along modes from n to k ) in one graph ?

The total fluctuation is the sum of the fluctuations along all the
modes. To get what you want, you just need to some the fluctuations.
Alternatively, you can filter a trajectory using a set of modes and do
further analysis on that.

> 2- Is there any way to obtain fluctuations of C-alpha atoms or backbone only
> from full atomic model ?

See the answer above.

> but I can chose only full atomic representation of the system consisted of
> 6518 atoms and any other selection would produce error.
> Is there any other way to obtain fluctuations on reduced number of atoms
> from full-atomic system ?

g_anaeig needs the atoms to match with the eigenvectors, which pertain
to the full set of atoms.

> 3- Also I've done two different NMA from one reference ( for full atomic
> model and for C-alpha mode).
> The overal picture of RMSF for instance was overal in both of the analysis
> but in case of the C-alpha only ANM RMSF were bigger in 10 times (0.02 Nm in
> case of full atomic NMA vs 2 NM in case of C-alpha NMA on equat residues).
> Why that difference might occur? Is there any way to increase amplitude of
> fluctuations by the temperature rising for instance ?

The c-alphas are less hindered in the second model due to the absence
of the side chains and such. There's just more freedom.



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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