exercises:2017_uzh_acpc2:prot_fol
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exercises:2017_uzh_acpc2:prot_fol [2017/05/17 12:40] – [Task 3: Evaluate the free energy difference and plot unfolding energy profile] vrybkin | exercises:2017_uzh_acpc2:prot_fol [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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===== Background ===== | ===== Background ===== | ||
- | A model protein you will have to deal with is the alanine decapeptide. The folding/ | + | A model protein you will have to deal with is the alanine decapeptide. The folding/ |
\begin{equation} | \begin{equation} | ||
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Rattle Lagrangian Multipliers: | Rattle Lagrangian Multipliers: | ||
</ | </ | ||
+ | |||
+ | <note warning> | ||
+ | Make sure that you get the units right. The Largange multipliers are written in atomic units (Hartree/ | ||
+ | </ | ||
* From these files you can calculate the average Lagrange multiplier of the Shake-algorithm like this: | * From these files you can calculate the average Lagrange multiplier of the Shake-algorithm like this: | ||
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* From these forces the free energy difference can be obtained via TI (see **Background**) | * From these forces the free energy difference can be obtained via TI (see **Background**) | ||
- | < | + | |
- | Make sure that you get the units right. The Largange multipliers are written in atomic units (Hartree/ | + | < |
+ | * Calculate $\Delta A$ numerically using the trapezoidal rule (or equivalent) with EXCEL, ORIGIN or any scripting language. | ||
</ | </ | ||
+ | |||
exercises/2017_uzh_acpc2/prot_fol.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1