[gmx-users] Normal mode analysis after equilibration

[Mario Fernández Pendás]

Dear All,

I am running simulations of a toxin placed in the middle of a bilayer. It
is known from the experiments that the equilibrium point of the toxin is in
one of the surfaces of the membrane.
I run MD with v-rescale a number of time-steps big enough to get the system
equilibrated with the toxin in the proper place.

At this stage, if I try to construct the Hessian matrix aiming to get its
eigenvalues without any energy minimization, it is likely that such
eigenvalues will be negative, isn't it? Even considering smaller time-steps
or tolerance?
By now, all my experiments confirm this trend so my question is to confirm
that I am not missing something.

Thank you very much.

Best,
Mario