[gmx-users] NMA eigenvectors doubts

Tue May 16 10:30:43 CEST 2017

Thanks Mark.. I am going to check all the input from the normal mode calculation.

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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