[gmx-users] NMA for a group

Bert de Groot bgroot at gwdg.de
Fri Jun 22 13:10:43 CEST 2007

Mark Abraham wrote:
> Christian Seifert wrote:
>> On Friday 22 June 2007 10:59, Bert de Groot wrote:
>> The hessian is the second (numerical) derivative of the atoms in the
>> three dimensions. In the future, I want to calculate the hessian of
>> molecules next to proteins, so the "small droplet of explicit water"
>> will not work here.  I do not understand, why I need to calculate the
>> second derivatives of the atoms of the whole system, if I just need it
>> of a small molecule.
> Er, technically the second derivative of the energy of the whole system
> with respect to the coordinates of the atoms, but I'm sure you know that
> :-) You could certainly produce an algorithm to do this for just a
> subset of atoms' coordinates, but so far I guess it hasn't been done
> because people haven't perceived any value in it. So if you're convinced
> it's a useful thing to do, you can either calculate the lot and extract
> the ones you want, or rework the code.

In addition, be aware that you should expect some negative eigenvalues in such a
case as for the subsystem you're most likely not in a minimum anymore. As Mark
and David already noted it's not immediately clear which physical interpretation
would correspond to such an approach.


Bert de Groot, PhD

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

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