[gmx-developers] Adding extra Potential Term and Force calculation in simulation

[Mark Abraham]

On 23/01/2012 9:21 PM, Trigo Mourino, Pablo wrote:
> Hi all, I want to modify the mdrun process in such a way we can add and extra
> Potential Energy term and their gradient in a orientational-dependent way.
> So, I think I need to make a group of atoms for define a plane (new
> molecule-fixed frame of reference) which normal orientation is going to be
> linked to the Energy difference during the simulation.

Have a look at how the effect of an external electric field is 
implemented in calc_f_el(). Get a debugger and step through mdrun to see 
how things work. Read section 3.4 of the manual first.

> Also I want to add to the Force term a way to calculate an extra force
> parameter which one atom is exerting under their neighbors (as a derivative
> regarding the new molecule-fixed frame of reference absolute orientation).

I have no idea what you mean here.

> Looking at similar questions in the list I think we need to modify  some
> kernel files and add new loops to take into account these extra potential in
> the derivation of forces. Can you direct me to the specific files and general
> loops we need to modify?

You should not touch the kernels unless you have an atomic pairwise 
interaction.

Mark