[gmx-users] Normal Modes

[Erik Lindahl]

Hi,

>
> The values of the negative eigenvalues after g_anaeig anlysis are:
>
>    -0.00056073
>    -0.00406724
>    -0.00636182
>
> These values really means that the protein is not in an energy well?
> Should I do an even better minimization?

It depends. You will always have 6 eigenvalues that should be  
numerically zero - translation and rotation of the entire system.

As long as the first six eigenvalues are close to zero and clearly of  
lower magnitude than the rest you are fine.

Cheers,

Erik

-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214