[gmx-users] negative eigenvalues occured and not "nearly zero"
silvester.thu
silvester.thu at gmail.com
Fri Apr 25 13:50:15 CEST 2008
Thanks David!
I have set constraints=none in .mdp file, and include the .trr file with -t option
With my best regards.
Yue Shao
2008-04-25
___________________________________________________________________________
___________________________________________________________________________
Shao Yue
Institue of Biomechanics and Biomedical Engineering
Department of Engineering Mechanics
Tsinghua University
P.R. China
____________________________________________________________________________
____________________________________________________________________________
发件人： David van der Spoel
发送时间： 2008-04-25 19:44:01
收件人： Discussion list for GROMACS users
抄送：
主题： Re: [gmx-users] negative eigenvalues occured and not "nearly zero"
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:
>
> 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:
> 1 0.000438558
> 2 -0.000683771
> 3 -0.00292664
> 4 0.00597364
> 5 0.00817211
> 6 -0.0114438
> 7 1.58334
> 8 1.80916
> 9 2.04356
> 10 2.6188
> 11 2.87512
> 12 3.44095
>
> 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?
Could it be that you used the coordinates from the .gro file for the nm
calculations?
Since these are rounded they may not correspond to the energy minimum.
You can use the grompp -t option to get binary coordinates.
Also, have you turned off constraints?
>
> 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.
>
> Yue Shao
>
> 2008-04-25
>
> ___________________________________________________________________________
> ___________________________________________________________________________
> **
> *Shao Yue*
> Institue of Biomechanics and Biomedical Engineering
> Department of Engineering Mechanics
> Tsinghua University
> P.R. China
> ____________________________________________________________________________
>
> ____________________________________________________________________________
>
>
> *发件人：* Mark Abraham
> *发送时间：* 2008-04-25 19:11:14
> *收件人：* Discussion list for GROMACS users
> *抄送：*
> *主题：* Re: [gmx-users] negative eigenvalues occured and not "nearly zero"
>
> silvester.thu wrote:
> > 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
> > morning.
>
> 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.
>
> Mark
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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