Negative eigen values while doing NMA of protein

[Pooja1]

I did the NMA of protein using gromacs. I created Heissen matrix and upon diagonalization of the heissen matrix, I chose to get 100 eigen values, eigen frequencies and eigen vectors. But, the first 93 eigen values are -ve and rest are positive. For eigen frequencies, first 93 eigen frequencies are 0’s and rest have some values. This doesn’t seem normal. What could be the reasons behind this?