[gmx-users] NMA eigenvectors doubts

Peter Stern peter.stern at weizmann.ac.il
Mon May 15 23:24:08 CEST 2017

Perhaps just the eigenvectors for the Calpha atoms.


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!!


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