[gmx-users] Normal Mode Analysis

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 10 07:51:59 CET 2011

On 10/11/2011 5:36 PM, James Starlight wrote:
> Thank you, Mark.
> By the way, also I have some question about data analysing
> From g_anaeig  I can obtain atom fluctuations along defined mode
> 1- Can I obtain same fluctuations along ensemble of several modes (i.e 
> averaged fluctuations along modes from n to k ) in one graph ?

Yes, through suitable use of your graphing program on multiple input 
files. IMO that would not be a suitable discussion for this list. 
Suggestions for graphing programs and some tricks of the trade are on 
the GROMACS webpage.

> 2- Is there any way to obtain fluctuations of C-alpha atoms or 
> backbone only from full atomic model ?
> E.g on start g_anaeig ask me
> Select an index group of 6518 elements that corresponds to the 
> eigenvectors
> Group     0 (         System) has  6518 elements
> Group     1 (        Protein) has  6518 elements
> Group     2 (      Protein-H) has  3269 elements
> Group     3 (        C-alpha) has   413 elements
> Group     4 (       Backbone) has  1239 elements
> ...
> 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 ?

Unless g_nmeig can be persuaded to calculate on a subset of the Hessian, 
I would guess not.

> 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?

 From your description, I think you're comparing apples with oranges.

> Is there any way to increase amplitude of fluctuations by the 
> temperature rising for instance ?

  NMA is athermal.


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