[gmx-users] simulating chemical reactions

[Mark Abraham]

gfunch wrote:
> Hi,
> Please excuse my ignorance as I am a complete newbie at MD simulations.
> 
> I am interested in simulating the 'gross' reaction of molecules in a
> (more-or-less aqueous) medium.
> Basically, I will have a number of 'A' molecules and some 'B'
> molecules. I would like to create 'C' molecules when 'A' and 'B' get
> within a certain distance of each other and depending upon a
> probability related to the reaction rate. I would like 'A', 'B', and

Conventional molecular MD software won't permit this, because the 
physical models that exist are not effective for modeling bond-breaking 
or bond-forming.  Thus you can't "want" to change A and B into C in any 
meaningful way.

> 'C' molecules to be able to diffuse through the medium and would also
> like the ability to put certain immobile 'obstacles' in the medium.

> I plan to ignore the atomic constituents of each molecule, and model
> each molecule as a particle with a certain size, shape, and charge.

It sounds like you need a much more flexible simulation platform that 
I've ever heard of for biomolecular MD.

> I can build a Monte Carlo simulation to simulate this scenario to some
> extent, but was wondering if I can use Gromacs to provide a platform
> that I can use to develop more sophisticated and accurate simulations.

GROMACS also doesn't do Monte Carlo simulations.

Mark