free energy changes of one subunit

From: Lixia Jin Day (ljin12_at_asu.edu)
Date: Tue Mar 16 2010 - 13:39:55 CDT

I collected simulation data for a protein complex in water for over 100ns.
Now I want to focus on one subunit or domain and calculate the free energy
changes during the 100ns due to the conformational changes in this subunit
or one of its domains. No reactions will be included, only conformational
changes. Can any one give me some advices on how to perform this with NAMD?
Thank you very much!

Lixia

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