[gmx-users] Normal Modes Analysis

[Fabrizio Mancinelli]

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? 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?
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})?
Thanks in advance.