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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