[gmx-users] NMA eigenvectors doubts

[Peter Stern]

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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