exercises:2018_uzh_acpc2:prot_fol
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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 [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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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 | + | 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. |
{{ : | {{ : | ||
===== 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 '' | + | Here you are asked to run several |
- | We have made this process automatic. To run TI for different values of the constraint, execute | + | We have made the script '' |
<code - run_ti_jobs.sh > | <code - run_ti_jobs.sh > | ||
Line 115: | Line 115: | ||
<note tip> | <note tip> | ||
- | * We have provided you with a useful script called '' | + | * We have provided you with a useful script called '' |
* 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. | * 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. |
exercises/2018_uzh_acpc2/prot_fol.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1