[gmx-users] Negative eigenvalues in normal mode analysis

[jjvc]

I'm doing a normal mode analysis of my protein (1FLT) but some eigenvalues are 
negative.
I did an energy minimization in 15 steps using l-bfgs minimizer until the norm 
of the force reach the value of  1.67842228266599e-09 and the maximum force 
is 9.42625899014056e-09

The values of the negative eigenvalues are:

   -0.00056073
   -0.00406724
   -0.00636182

These values really means that the protein is not in an energy well?
Should I do an even better minimization?

Thanks
jjvc