[gmx-users] normal mode analysis.

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Mon Mar 3 11:29:25 CET 2003


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




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