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exercises:2017_uzh_acpc2:prot_fol [2017/05/17 12:32] – [Task 2: Perform constrained MD simulations] 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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 </note> </note>
  
 +==== Constraint section TO BE modified for constrained MD ====
 +<code - constraint section>
 + &CONSTRAINT
 +    &COLLECTIVE
 +      COLVAR 1
 +      INTERMOLECULAR
 +      TARGET [angstrom] 18.36
 +    &END COLLECTIVE
 +    &LAGRANGE_MULTIPLIERS
 +      COMMON_ITERATION_LEVELS 1
 +    &END
 + &END CONSTRAINT
 +</code>
 +
 +===== 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>
-Shake  Lagrangian Multipliers:            -0.054769270 +Shake  Lagrangian Multipliers:           -63.547262596 
-Rattle Lagrangian Multipliers:            -0.020937479 +Rattle Lagrangian Multipliers:            63.240598387 
-Shake  Lagrangian Multipliers:            -0.020937479 +Shake  Lagrangian Multipliers:            -0.326901815 
-Rattle Lagrangian Multipliers:            -0.020937479 +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>
  
-==== Constraint section TO BE modified for constrained MD ==== +
-<code - constraint section> +
- &CONSTRAINT +
-    &COLLECTIVE +
-      COLVAR 1 +
-      INTERMOLECULAR +
-      TARGET [angstrom] 18.36 +
-    &END COLLECTIVE +
-    &LAGRANGE_MULTIPLIERS +
-      COMMON_ITERATION_LEVELS 1 +
-    &END +
- &END CONSTRAINT +
-</code>+
exercises/2017_uzh_acpc2/prot_fol.1495024340.txt.gz · Last modified: 2020/08/21 10:15 (external edit)