[gmx-users] Hessian instability

[Tomas Kubar]

Ignacio Rodriguez Fernandez wrote:

>Hello,
>
>I´m trying perform a normal mode analysis of a large molecule. My problem is
>that I always get negative eigenvalues, which shouldn´t happen in theory.
>The problem seems to be the instability of the Hessian matrix, due to an
>unproper minimization of the molecule. I have already tried some
>minimization algorithms (steepest descent, conjugate gradients, l-bfgs,
>etc)for GROMACS but they all seem to fail.
>
>Do you know the real cause of this problem and how could be avoided?
>
>  
>
hi
it may be caused by an insufficient precision of the coordinate file 
that you have read in. you can try to read a full-precision trajectory 
from minimization (-t option for grompp).
tomas

>Thanks,
>
>Ignacio
>
>
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