[gmx-users] Normal mode analysis after equilibration

[David van der Spoel]

On 14/01/16 18:23, Mario Fernández Pendás wrote:
> 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.
What is an "equilibrium point"?

> 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?
Yes you are bound to get negative eigenvalues.

Why would you want to do NM of part of a complex system anyway? You will 
suddenly throw away all the correlations with the membrane and solvent.

In my opinion normal mode analysis virtually only makes sense for 
isolated systems in the gas-phase

> 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
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se