[gmx-users] reg binding free energy

[Erik Marklund]

On Mar 7, 2013, at 2:59 AM, Justin Lemkul wrote:

>
> On 3/6/13 8:57 PM, Vishwambhar Bhandare wrote:
>> dear gromacs user,
>> how i can do binding free energy calculation for RNA duplex in  
>> gromacs?
>> any tutorial for the same??
>
> Free energy calculations involving interactions between  
> macromolecules are typically done with umbrella sampling.  A  
> tutorial is linked from gromacs.org, otherwise refer to the  
> literature for suggested methodology.

The challenge is likely to find a proper reaction coordinate and  
assure that you sample sufficiently along it. You may end up wasting a  
lot of computer time if you make a poor choice.

Erik