[gmx-users] NMA eigenvectors doubts

[Mark Abraham]

On Wed, May 17, 2017 at 11:15 AM luca maggi <maggi_luca at hotmail.it> wrote:

> 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.
>
>
Memory doesn't partly allocate. You get all of what you ask for, or none of
it. The most likely reason is that it matches the amount you need for what
you asked for, which comes back to which groups you used when you set up
inputs, wrote outputs, etc.

You probably only want the eigenvectors from the solute anyway, so do that.

Mark