[gmx-users] negative eigenvalues occured and not "nearly zero"

[Mark Abraham]

silvester.thu wrote:
> Thanks Mark.
> I also have doubted that the system was not at the minium stationary 
> point before, because I searched the mailing-list archive and found the 
> description below:

>  
> The author of this description was describing another problem which was 
> different from my question. But this descripment is helpful for me. In 
> this description, the author minimized the energy of the system to reach 
> the level -- Fmax<1e-9 -- which I do not know how to get to. I have 

Depending what termination criterion was satisfied in your EM, you might
do better by increasing the number of steps, or decreasing the emtol
.mdp file parameter (see manual 7.3)

> tried my best to EM, but I only got Fmax<3e-4. In the mdrun_d step, 
> there is no warning, while in the g_nmeig_d step, there is a warning that
>  
> /One of the lowest 6 eigenvalues has a non-zero value.
> This could mean that the reference structure was not
> properly energy minimized./
>  
> So the system may be not at the minimum stationary point. How can I make 
> the system to reach this point?

As I suggested last time, perturbing it in a sensible manner and
observing the behaviour is a way to test your minimization.

Mark