[gmx-users] NMA eigenvectors doubts

[luca maggi]

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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