[gmx-users] NMA eigenvectors doubts

Wed May 17 10:17:53 CEST 2017

Hi,

I suspect the issue is related to the previous warning that you haven't
minimized well enough. The diagonalization won't produce a full set of
normal modes if the input coordinates are not at a stationary point.
(Caveat, I've never used the method...)

Mark

On Wed, May 17, 2017 at 9:36 AM luca maggi <maggi_luca at hotmail.it> wrote:

> Maybe I figured the problem out!! The point is that my system is too big.
> I tried to minimize just the protein (6908 atoms) and the number of the
> matrix and the entries of the eigenvectors fit with the number of my
> system...I think Gromacs can not deal with system bigger than 15k atoms for
> the normal mode analysis :(...Do you think it is rigth??
>
> is there any possibility to solve this issue??
>
>
> Luca
>
>
> ________________________________
> Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> per conto di luca
> maggi <maggi_luca at hotmail.it>
> Inviato: martedì 16 maggio 2017 11.12
> A: gmx-users at gromacs.org
> Oggetto: Re: [gmx-users] NMA eigenvectors doubts
>
> During the calculation of the hessian matrix (the mdrun step) gromacs
> gives me the output:
>
> "
>
> There are: 127659 Atoms
>
> Non-cutoff electrostatics used, forcing full Hessian format.
>
> Allocating Hessian memory...
>
>
> starting normal mode calculation 'Protein in water'
>
> 15904 steps.
>
>
> Maximum force: 1.64976e-02
>
> The force is probably not small enough to ensure that you are at a minimum.
>
> Be aware that negative eigenvalues may occur
>
> when the resulting matrix is diagonalized
>
>
> Finished step 1690 out of 7952"
>
>
> At this stage it comes out with this weird number...I don't konow if it
> could be helpful!
>
> The command I used is simply:
>
>
> gmx_mpi_d mdrun  -deffnm nm_calc_67 -v -ntomp 32
>
>
> Best
>
> Luca
>
> ________________________________
> Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> per conto di Mark
> Abraham <mark.j.abraham at gmail.com>
> Inviato: martedì 16 maggio 2017 10.25
> A: gmx-users at gromacs.org
> Oggetto: Re: [gmx-users] NMA eigenvectors doubts
>
> Hi,
>
> I suggest you go back through your workflow, paying attention to any time
> you selected a group of atoms for output or analysis, and reading carefully
> through the outputs of the various tools. If the output isn't what you
> expect... reconsider the input. :-)
>
> Mark
>
> On Tue, May 16, 2017 at 9:05 AM luca maggi <maggi_luca at hotmail.it> wrote:
>
> > The protein atoms are  6908. I have a membrane  with 35884 atoms and
> water
> > 84696. So far I calculated only the first eigenvector but as I said I
> > can't  understand why the number of row  of this vector is 7952 or so.
> >
> >
> > Luca
> >
> > ________________________________
> > Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> per conto di Peter
> > Stern <peter.stern at weizmann.ac.il>
> > Inviato: martedì 16 maggio 2017 08.25
> > A: gmx-users at gromacs.org
> > Oggetto: Re: [gmx-users] NMA eigenvectors doubts
> >
> > How many protein atoms do you have?  How many eigenvectors?  The program
> > is not going to calculate the normal modes of the water molecules.
> >
> > Peter
> >
> > Sent from my iPhone
> >
> > > On May 16, 2017, at 8:53 AM, luca maggi <maggi_luca at hotmail.it> wrote:
> > >
> > > Hi Peter,
> > >
> > > Thanks  for your answer...but my system is composed by a protein and  a
> > membrane plus the water. The  Calphas are just 438, so I don't think that
> > number is referred to alpha carbons. Moreover I didn't set my calculation
> > in order to calculate the  Calpha eigenvectors...
> > >
> > >
> > >
> > > ________________________________
> > > Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> per conto di Peter
> > Stern <peter.stern at weizmann.ac.il>
> > > Inviato: lunedì 15 maggio 2017 23.14
> > > A: gmx-users at gromacs.org
> > > Oggetto: Re: [gmx-users] NMA eigenvectors doubts
> > >
> > > Perhaps just the eigenvectors for the Calpha atoms.
> > >
> > > Peter
> > >
> > > Sent from my iPhone
> > >
> > > On May 15, 2017, at 9:30 PM, luca maggi <maggi_luca at hotmail.it<mailto:
> > maggi_luca at hotmail.it>> wrote:
> > >
> > > Dear Gromacs Users,
> > >
> > >
> > > I have performed a normal mode analysis with gromacs. I have calculated
> > the hessian matrix and the related eigenvalues and eigenvectors. At this
> > point  I needed to extract some elements from the  eigenvectors  and
> using
> > the dump tool of gromacs I wrote the first of them in a file, but I
> > realised something unexpected. The vector is composed by 7952 row and
> three
> > columns. My system is composed by about 127000 atoms, thus I expected to
> > find a vector with 127000 x 3 entries...but this number (7952) does not
> fit
> > at all with my expectation. It seems to be related with the number of
> steps
> > performed during the normal mode analysis but i cannot understand why????
> > >
> > > How has this vector been calculated ?????
> > >
> > >
> > > Suggestion and hints would be really appreciated!!
> > >
> > >
> > > Thanks
> > >
> > >
> > > Luca
> > > --
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