[gmx-users] Hessian instability
tomas.kubar at uochb.cas.cz
Tue Mar 7 18:39:56 CET 2006
Ignacio Rodriguez Fernandez wrote:
>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?
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).
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