[gmx-users] Loop displacement calculation?

[Mark Abraham]

SeungPyo Hong wrote:
> Thank you for your kind response.
> 
> I think that I do not clearly describe the system.
> 
> The loop I mentioned above seems to interact with the other parts of the 
> protein with hydrophobic interactions.
> So, the displacement of the loop from the original position will make 
> the free energy difference, and this can estimate the energy stabilized 
> by the loop placement on its natural form.
> 
> Is this statement seems to be reasonable?

That makes a lot more sense, however I don't have the expertise to judge 
whether there's a better method around.

> Frankly I am not understanding the free energy calculation method, and 
> maybe it is the reason why I think that this simulation works.
> I premised that if the free energy code really calculate the free energy 
> a certain ensenble of microstates, it can be used to test the stability 
> of the part of the protein.

Follow the links here 
http://wiki.gromacs.org/index.php/Special:Search?search=free+energy&go=Go 
for some tutorial material. Obviously, you will only ever calculate free 
energy *differences*.

Mark