[AMBER] capturing free energy landscape

From: anu chandra <anu80125.gmail.com>
Date: Tue, 10 Dec 2013 15:53:46 +0530

Dear Amber users,

I am working with all-atom MD simulations of protein-ligand system. I have
carried out PCA analysis after 75ns of simulation. By looking at the
collective motions along the first principle component, I could able to see
that the protein is visiting two different conformations.Now, I am looking
for a method to capture the free energy landscape of these conformational
changes. If I am right, usual methodologies like meta-dynamics. AMD etc.
are usually used to overcome the high energy barrier during the
conformational changes. Since I could capture the conformational changes in
my protein during the classical MD itself, it seems like the energy barrier
is too low between these two different conformations. How can I capture
free energy change during these conformational changes? Which method will
be helpful for me to do this calculation?

Waiting for your valuable reply.

Thanks in advance

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Received on Tue Dec 10 2013 - 02:30:02 PST
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