exercises:2018_uzh_acpc2:prot_fol
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revision | Next revisionBoth sides next revision | ||
exercises:2018_uzh_acpc2:prot_fol [2018/05/18 21:10] – [Task 1: Familiarize yourself] gtocci | exercises:2018_uzh_acpc2:prot_fol [2018/05/18 21:11] – [Task 3: Evaluate the free energy difference] gtocci | ||
---|---|---|---|
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