[gmx-users] negative eigenvalues occured and not "nearly zero"
silvester.thu at gmail.com
Fri Apr 25 13:31:15 CEST 2008
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:
I have checked the first eigenvalues in .xvg files, some of them really large.
For example, a 88 amino acid protein (PDB ID=1krn), there are 79 amino
acid coordinates in the PDB file. After EM, the Max force< 1e-9, while the
first 12 eigenvalues g_nmeig_d worked out are:
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 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?
What's more, in the description above, the first six eigenvalues are very near to zero, and that is what I want now, because as I said before, I can not get such "nearly zero" eigenvalues.
So, if you know how to do the EM to such a low energy level, or how to get those "nearly zero" eigenvalues, please give me some advice or some examples.
Thanks a lot for your attentions!
With my best regards.
Institue of Biomechanics and Biomedical Engineering
Department of Engineering Mechanics
发件人： Mark Abraham
发送时间： 2008-04-25 19:11:14
收件人： Discussion list for GROMACS users
主题： Re: [gmx-users] negative eigenvalues occured and not "nearly zero"
> 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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