[gmx-users] Free energy of conformation

[esther]

Hello,
I didn't get a response to this question before, so here I go again: I have
a protein that has a residue modeled as a 2-state rotamer in the crystal
structure. The transition occurs in ms, so I cannot see it in the MD
simulations. I'd like to calculate the free energy difference between both
states, possibly using the perturbation method. But I am not sure how to do
this, as examples are usually done for mutations and hydration. Has anyone
an idea of how to do this? So far I have thought of changing the dihedral of
the side chain in the top file (which goes from avge -90 to 90), but I am
thinking that maybe there are other things that I need to account for. Any
ideas 
?
Thanks!!

Esther Caballero-Manrique
Graduate Teaching Fellow
Chemistry Department
1253 University of Oregon
Eugene, OR 97403-1253
(541) 346-2485
 

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