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
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