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--- exercises:2017_uzh_acpc2:prot_fol [2017/05/17 12:40] – [Task 3: Evaluate the free energy difference] vrybkin
+++ exercises:2017_uzh_acpc2:prot_fol [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 ===== Background =====
-A model protein you will have to deal with is the alanine decapeptide. The folding/unfolding will be achieved by fixing the distance between the end carbon atoms in the chain: atoms 7 and 98. This distance is called a collective variable. At each distance one runs the MD simulation (constrained MD) to extract the time-averaged forces acting on the collective variable, $F(x)$. Then, a free energy difference can be calculated via thermodynamic integration (TI):
+A model protein you will have to deal with is the alanine decapeptide. The folding/unfolding will be achieved by stretching/compressing the chain and fixing the distance between the end carbon atoms in it: atoms 7 and 98. This distance is called a collective variable. At each distance one runs the MD simulation (constrained MD) to extract the time-averaged forces acting on the collective variable, $F(x)$. Then, a free energy difference can be calculated via thermodynamic integration (TI):
 \begin{equation}
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   * From these forces the free energy difference can be obtained via TI (see **Background**)
+<note tip>
+  * Calculate $\Delta A$ numerically using the trapezoidal rule (or equivalent) with EXCEL, ORIGIN or any scripting language.
+</note>