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--- exercises:2018_uzh_acpc2:prot_fol [2018/05/18 21:09] – [Task 2: Perform constrained MD simulations] gtocci
+++ exercises:2018_uzh_acpc2:prot_fol [2018/05/18 21:11] – [Task 3: Evaluate the free energy difference] gtocci
@@ Line 27: / Line 27: @@
 Although the image below shows the deca-alanine in water, it is expensive to run thermodynamic integration
- for a solvated protein with many values  of the constraints (here we choose 5 to 10) on small laptops. So we will run TI for the protein in the gas-phase.
+ for a solvated protein with many values of the constraints on small laptops. So we will run TI for the protein in the gas-phase.
 {{ :exercises:2017_uzh_acpc2:deca_ala.gif?400 |}}
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 <note tip>
-  *  We have provided you with a useful script called ''generate_plots.sh'' that extracts the average force and the standard error for each constrained MD simulation (see the ''grep'' command line above), and it prints out the file ''force_vs_x.dat'' containing the force as a function of the collective variable, and the error on the force (third column). Take a look at the script and modify it if necessary, e.g. if you have changed the lower and upper bound for the constraint or if you have changed the number of constraints.
+  *  We have provided you with a useful script called ''generate_plots.sh'' that extracts the average force and the standard error for each constrained MD simulation (see the ''grep'' command line above), and it prints out the file ''av_force_vs_x.dat'' containing the force as a function of the collective variable, and the error on the force (third column). Take a look at the script and modify it if necessary, e.g. if you have changed the lower and upper bound for the constraint or if you have changed the number of constraints.
   * In order to check the convergence of the free energy profile one should look at the error on the average force for each constrained MD simulation. The error on the free energy profile can be obtained by propagating the error on the average force upon integration.
   * From the file containing the average force as a function of collective variable you need to integrate $F(x) dx$ numerically to obtain $\Delta A$. You may use the trapezoidal rule (or equivalent) with EXCEL, ORIGIN or any scripting language.