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--- exercises:2018_uzh_acpc2:prot_fol [2018/05/18 19:40] – [Task 2: Perform constrained MD simulations] gtocci
+++ exercises:2018_uzh_acpc2:prot_fol [2018/05/18 20:05] – [Task 1: Familiarize yourself] gtocci
@@ Line 14: / Line 14: @@
 Download the files: {{ :exercises:2018_uzh_acpc2:deca_ala_ex3.tar.gz |}}
-in the directory "deca_ala" you will find
+in the directory ''deca_ala'' you will find
 ''deca_ala.pdb'' (protein data base) file contains the coordinates
@@ Line 93: / Line 93: @@
 </code>
-  * The average Lagrange multiplier is the average force $F(x)$ required to constrain the atoms at the distance $x$.
+  * The average Lagrange multiplier is the average force $F(x)$ required to constrain the atoms at the distance $x$. First of all, plot the force $F(x)$ with its standard error as a function of the collective variable to see if the simulation carried out so far is statistically relevant or the relative error is too large.
-  * From these forces the free energy difference can be obtained via thermodynamic integration between the two states. Given that state $a$ and $b$ are the initial and the final values of the collective variable, extract the free energy difference from
+  * From the forces, the free energy difference can be obtained via thermodynamic integration between the two states. Given that state $a$ and $b$ are the initial and the final values of the collective variable, extract the free energy difference from
 \begin{equation}
@@ Line 115: / Line 115: @@
 <note tip>
-  *  We have provided you with a useful script called ''generate_plots.sh'' that extracts the average force for each constrained MD simulation, and it prints out the file ''force_vs_x.dat'' containing the force as a function of the collective variable. 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 ''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.
 </note>