[gmx-users] negative eigenvalues occured and not "nearly zero"
Mark.Abraham at anu.edu.au
Fri Apr 25 15:22:04 CEST 2008
> 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.
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