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--- exercises:2018_uzh_acpc2:prot_fol [2018/05/18 21:10] – [Task 1: Familiarize yourself] gtocci
+++ exercises:2018_uzh_acpc2:prot_fol [2018/05/18 21:21] – [Task 2: Perform constrained MD simulations] gtocci
@@ Line 32: / Line 32: @@
 ===== Task 2: Perform constrained MD simulations =====
-To perform thermodynamic integration one has to run MD for different values of the distance between atoms 11 and 91, in each run it will be constrained. In the original file ''md_std.inp'' it is set to $14.37$ Å as is in the ''deca_ala.pdb'' file.
+Here you are asked to run several MD simulations for different values of the distance between atoms 11 and 91, in each run it will be constrained. In the original file ''md_std.inp'' the distance is set to $14.37$ Å as is in the ''deca_ala.pdb'' file. This is the first step to carry out the termodynamic integration, as described in the equation above.
-We have made this process automatic. To run TI for different values of the constraint, execute the script ''run_ti_jobs.sh'' that you find inside the compressed file ''deca_ala.tar.gz''. Take a look at the script and familiarize yourself with it. At which values are we constraining the distances between the carbon atoms? In this case we are performing 5 different simulations, each with a different value of the constraint. Feel free to use a larger or smaller number of constraints and to increase or reduce the upper and/or lower bound.
+We have made the script ''run_ti_jobs.sh'' to run these simulations, which you can find inside the compressed file ''deca_ala.tar.gz''. Take a look at the script and familiarize yourself with it. At which values are we constraining the distances between the carbon atoms? In this case we are performing 5 different simulations, each with a different value of the constraint. You can edit this script to use a larger or smaller number of constraints and to increase or reduce the upper and/or lower bound of integration. Can you guess where in the script we are specifying the values of the constraints?
 <code - run_ti_jobs.sh >
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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.