[gmx-users] NMA for a group

[Mark Abraham]

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.

Mark