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exercises:2017_uzh_acpc2:prot_fol [2017/05/17 12:37] – vrybkinexercises: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/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} \begin{equation}
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 </code> </code>
  
-===== Task 3: Evaluate the free energy difference and plot unfolding energy profile =====+===== Task 3: Evaluate the free energy difference =====
 ⇒ Each constrained MD will produce a ''.LagrangeMultLog''-files, which look like this: ⇒ Each constrained MD will produce a ''.LagrangeMultLog''-files, which look like this:
 <code> <code>
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 Rattle Lagrangian Multipliers:            -0.318145579 Rattle Lagrangian Multipliers:            -0.318145579
 </code> </code>
 +
 +<note warning>
 +Make sure that you get the units right. The Largange multipliers are written in atomic units (Hartree/bohr), while the distances are in Angstrom.
 +</note>
  
   * 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**)
  
-<note warning> + 
-Make sure that you get the units right. The Largange multipliers are written in atomic units (Hartree/bohr), while the distances are in Angstrom.+<note tip> 
 +  * Calculate $\Delta A$ numerically using the trapezoidal rule (or equivalent) with EXCEL, ORIGIN or any scripting language.
 </note> </note>
 +
  
exercises/2017_uzh_acpc2/prot_fol.1495024634.txt.gz · Last modified: 2020/08/21 10:15 (external edit)