[gmx-users] Loop displacement calculation?

[Mark Abraham]

SeungPyo Hong wrote:
> Dear gmx-users,
> (This is not related to my previous question about the failure of the 
> simulation. Now I guess that there are some technical problems in our 
> cluster system.)
> 
> Hello gmx-users,  I am not a quite new user, but still don't know many 
> many thing.
> Planning an experiment I hope to listen to your advices.
> 
> Recently I plan to perform free energy calculation to test the stability 
> of a loop in a protein.
> To do so, I will select two atoms; one in the backbone atom of the loop 
> and the other in the backbone of the protein nearby the loop region.
> Then, those sites are connected by a [ bond ] and the spring constant 
> will be changed from 0 to 100 as lambda changes from 0 to 1. (The 
> equilibrium length is fixed to 20 A.)
> 
> I am wandering  whether this simulation will be generally accepted or not.

How does such a calculation reveal the "stability of [the] loop"? You 
need a more precise goal in order to design a calculation to measure 
something. Perhaps some more background reading is in order :-)

Mark