[gmx-users] Hessian instability

Ignacio Rodriguez Fernandez irf at soton.ac.uk
Fri Mar 3 14:40:28 CET 2006


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?



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