[gmx-users] Normal Modes Analysis

Bert de Groot bgroot at gwdg.de
Wed Oct 5 14:30:50 CEST 2005

Fabrizio Mancinelli wrote:
> Hi colleagues,
> I would like to have some delucidation, from your own experience,
> about performing an NMA.
> My system is an usual protein in water.
> After energy minimization (full precision, CG or L-BFGS), next step should be 
> Hessian calculation. The first question is: if I perform it on the whole 
> system (protein + SOL), isn't the matrix too big? 

it becomes quite big, yes. If it becomes "too" big depends on
the amount of RAM in yoru system. Including solvent in a NMA
is usually a good idea, but you may get away with just a shell of
water molecules. Remember that due to the minimisation criteria
(NMA only works in an absolute minimum), the use of PBC and
cut-offs is usually not recommended/possible, due to boundary
instabilities cutoff and/or box edge.

> On the other hand, this is 
> not what I want: I just need NMA on the backbone; but, by filtering off the 
> SOL coordinates prior to hessian calculation, don't I miscalculate the 
> hessian for my system?

yes, AFAIK, you need to pereform the Hessian coputation + diagonalisation
on the full system. There have been some recent discussions on performing
NMA on subsystems but I don't know the status on that. Maybe Berk can comment?

> Second question is, let's suppose I have correctly calculated and subseqeuntly 
> diagonalized the hessian. How can I get the frequency spectrum (in cm^{-1})?

the eigenvalues of the Hessian are the frequencies. Check the units though
(discussed before on this list).


Bert de Groot, PhD

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de

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