[gmx-users] NMA eigenvectors doubts

Wed May 17 11:14:51 CEST 2017

Hi Mark,

Thanks..But Even if I didn't minimized very well my system I can't understand why the calculation of the hessian is performed just on some of the total DoF. It is probably an issue of memory allocation. Indeed performing the same calculation just on  the protein (bad minimized Fmax=2.17e+02) It gives me the same error but It calculates  all the matrix entries anyway.

Thanks again

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: mercoledì 17 maggio 2017 10.17
A: gmx-users at gromacs.org
Oggetto: Re: [gmx-users] NMA eigenvectors doubts

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
> > > --
> > > Gromacs Users mailing list
> > >
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