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exercises:2018_uzh_acpc2:prot_fol [2018/05/18 20:03] – [Task 3: Evaluate the free energy difference] gtocciexercises:2018_uzh_acpc2:prot_fol [2018/05/18 21:10] – [Task 1: Familiarize yourself] gtocci
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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. +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. 
  
 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 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.
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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 ..
exercises/2018_uzh_acpc2/prot_fol.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1