[gmx-users] Re: DNA simulations

[Mark Abraham]

On 07/05/2012 01:04 PM, SatyaK wrote:
>   Thanks once again Mark. I am trying to figure out things. Basically, I am
> using ReaxFF for my simulations.

Has that been ported to GROMACS? If not, you have that issue to consider 
first.

>   The basic problem I want to address is, to
> place OH radicals as close as possible to the DNA and rest with water
> molecules in a box.

The same kind of approach is needed - you need a geometric criterion to 
split up the waters, etc.

Mark