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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jan 23 13:24:24 CET 2012

On 23/01/2012 11:14 PM, Trigo Mourino, Pablo wrote:
> On Jan 23, 2012, at 1:00 PM, Mark Abraham wrote:
>>> 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.
> The idea is, the energy of a different orientations for one group of 
> atoms is generating a force under the neighbor atoms in the molecule 
> and we want to introduce that force in the simulation. As far as I 
> know is maybe something similar to the implementation of pull code in 
> umbrella sampling but with the difference that the pull should be 
> energy-driven and no restrained along a vector as in:
>     *pull_geometry:*
>     **
>     .....
>         *position*
>             Pull to the position of the reference group plus
>             *pull_init* + time**pull_rate***pull_vec*.
>             ......

Something that actually is intra-molecular is probably best implemented 
as an (atypical) "bonded" interaction - again, don't touch the kernels. 
You need some way of working out what atoms will interact with what 
other atoms.

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