From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jun 16 2006 - 13:11:52 CDT
You'll have to use thermodynamic integration (see Mark Abraham's email
earlier today), umbrella sampling, or some similar method to do this
(you should be able to find good citations for those terms on google
scholar and the like); you cannot just extract free energy changes from
a single MD trajectory because the change in entropy cannot be
calculated from this information.
> I want to check how to chage free energy during molecular dynamics in
> the unfolding process.
> How can I do that?
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