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exercises:2018_uzh_acpc2:prot_fol [2018/05/18 19:38] – [Task 3: Evaluate the free energy difference] gtocciexercises:2018_uzh_acpc2:prot_fol [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 Download the files: {{ :exercises:2018_uzh_acpc2:deca_ala_ex3.tar.gz |}} 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  ''deca_ala.pdb'' (protein data base) file contains the coordinates 
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 Although the image below shows the deca-alanine in water, it is expensive to run thermodynamic integration  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 |}} {{ :exercises:2017_uzh_acpc2:deca_ala.gif?400 |}}
  
 ===== Task 2: Perform constrained MD simulations ===== ===== 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 $18.36$ 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 > <code - run_ti_jobs.sh >
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   cp deca_ala/* $d/.   cp deca_ala/* $d/.
   cd $d   cd $d
-  sed -e "s|18.36|${d}|" md_std.inp > d_${d}.inp+  sed -e "s|14.37|${d}|" md_std.inp > d_${d}.inp
   cp2k.sopt -i d_${d}.inp -o d_${d}.out    cp2k.sopt -i d_${d}.inp -o d_${d}.out 
   cd ..   cd ..
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 <note tip> <note tip>
   * Be careful with the values chosen for the upper and lower bound of the constraints as the simulations might crash or the SHAKE algorithm for the computation of the constraints might not converge if the values of the constrained distances are unphysical.   * Be careful with the values chosen for the upper and lower bound of the constraints as the simulations might crash or the SHAKE algorithm for the computation of the constraints might not converge if the values of the constrained distances are unphysical.
-  * We have set the number of steps of each constrained MD to 10000. Try to increase this number if you want to achieve better statistics or to decrease it to get the results faster, at the expense of a more converged free energy.+  * We have set the number of steps of each constrained MD to 5000. Try to increase this number if you want to achieve better statistics or to decrease it to get the results faster, at the expense of a more converged free energy.
 </note> </note>
  
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 </code> </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} \begin{equation}
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 <note tip>   <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 ''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.   * 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> </note>
exercises/2018_uzh_acpc2/prot_fol.1526672286.txt.gz · Last modified: 2020/08/21 10:15 (external edit)