[gmx-developers] regd do_fnbf() non bonded interaction calculation

[Erik Lindahl]

On Feb 4, 2004, at 4:22 PM, Anjan Raghunathan wrote:

> Hi,
>    Thanks for the suggestion.Will go with it.
>  One more Q...
> Suppose I need to change the particle itself that is being simulated 
> during the run of the simulation.
> For example, suppose potassium is being simulated in a fluid and after 
> a particular time or region I'd like to make it some other particle 
> say sodium.(Though this is artificial I really would like to know if 
> this procedure is possible).
>    So basically, how can I change the LJ parameters and the charge of 
> the particle inside the code in GROMACS?
>

That's usually done with "Free Energy" runs, i.e. you gradually change 
the type of one or several atoms during the run. It's fairly 
straightforward - you can find several examples by searching the list 
archives, or check the manual for details.

Cheers,

Erik