[gmx-users] normal mode analysis.

[Nguyen Hoang Phuong]

Dear All,

I used the GROMACS program to do normal mode analysis for my molecule in
vacuum. After energy minimization, Fmax = 10^-6. However, the eigenvectors
obtained from diagonalization of the Hessian at the lowest energy
structure (at Fmax = 10^-6) are not othogonal with each other. For
example, V1.V2 = 0.0006 where V1 and V2 are two eigenvectors. This number
is considered to be large compared to zero. Does anyone have the same
observation? Thanks.

Phuong