exercises:2018_uzh_acpc2:prot_fol
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
exercises:2018_uzh_acpc2:prot_fol [2018/05/18 21:09] – [Task 2: Perform constrained MD simulations] gtocci | exercises:2018_uzh_acpc2:prot_fol [2018/05/18 21:11] – [Task 3: Evaluate the free energy difference] gtocci | ||
---|---|---|---|
Line 27: | Line 27: | ||
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. |
{{ : | {{ : | ||
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