[gmx-users] Normal Modes Analysis

Erik Lindahl lindahl at sbc.su.se
Wed Oct 5 15:02:02 CEST 2005


Make sure you're using one of the 3.3 release candidate versions. the  
NMA code is significantly improved there, and uses sparse matrix  
storage to enable NMA calculations for huge systems.



On Oct 5, 2005, at 2:30 PM, Bert de Groot wrote:

> 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
> ________________________________________________
> 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
> http://www.mpibpc.mpg.de/groups/de_groot
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