[gmx-users] negative eigenvalues occured and not "nearly zero"
Mark.Abraham at anu.edu.au
Fri Apr 25 13:10:01 CEST 2008
> Hi Berk, thanks for your reply, but there are still problems.
> While the first six eigenvalues are corresponding to the three
> translational and three rotational dimensions of freedom of the whole
> system, they should be zero (theoretically) or at least not
> much different from zero (e.g: 1e-3 or -1e-3). But in my problem, I
> encountered some negative values that are much different from zero, as I
> listed before.
> And I have used the g_nmtraj_d to generate and visualize the modes
> corresponding to those negative eigenvalues, and I found that those
> modes were neither translational nor rotational movements -- they were
> actually "oscillational movements". It is unreasonable. So I guess there
> might be something wrong in my calculation. But, I still can not figure
> out what is wrong, even after I discussed with members in my group this
I don't have much experience in such a calculation with an MM force
field, but such Hessian eigenvalues in quantum chemistry indicate that
you are at some non-minimum stationary point. That seems unlikely for an
MM EM calculation, unless the PES is very flat. I can't guess what
"oscillational movements" are, but if you perturb the system in the
direction of that eigenvector (easy if it's mostly on a few atoms,
otherwise just add a suitable multiple of the eigenvector to the atom
coordinate vector) you can see if you get into the range of a suitable
local minimum, or return to your existing stationary point.
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