exercises:2017_uzh_acpc2:prot_fol
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exercises:2017_uzh_acpc2:prot_fol [2017/05/17 12:13] – [Task 1: Familiarize yourself] vrybkin | exercises:2017_uzh_acpc2:prot_fol [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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===== Background ===== | ===== Background ===== | ||
- | A model protein you will have to deal with is the alanine decapeptide. The folding/ | + | A model protein you will have to deal with is the alanine decapeptide. The folding/ |
\begin{equation} | \begin{equation} | ||
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===== Task 2: Perform constrained MD simulations ===== | ===== Task 2: Perform constrained MD simulations ===== | ||
For that you have to run MD for different values of the distance between atoms 7 and 98, in each run it will be constrained. In the original file '' | For that you have to run MD for different values of the distance between atoms 7 and 98, in each run it will be constrained. In the original file '' | ||
+ | |||
+ | - Run CP2K with '' | ||
+ | - Copy '' | ||
+ | - Modify the PROJECT_NAME and '' | ||
+ | - Run CP2K with the new input file; | ||
+ | - Repeat for several values in the range $15$ to $20 $ Å. | ||
+ | |||
+ | <note tip> | ||
+ | * To avoid confusion, try to perfrom every task in a new directory | ||
+ | * You may increase or decrease the number of MD steps, which is set to 5000 in the file, to speed-up the calculation or else get a better statiscics. | ||
+ | </ | ||
+ | |||
+ | ==== Constraint section TO BE modified for constrained MD ==== | ||
+ | <code - constraint section> | ||
+ | & | ||
+ | & | ||
+ | COLVAR 1 | ||
+ | INTERMOLECULAR | ||
+ | TARGET [angstrom] 18.36 | ||
+ | &END COLLECTIVE | ||
+ | & | ||
+ | COMMON_ITERATION_LEVELS 1 | ||
+ | &END | ||
+ | & | ||
+ | </ | ||
+ | |||
+ | ===== Task 3: Evaluate the free energy difference ===== | ||
+ | ⇒ Each constrained MD will produce a '' | ||
+ | < | ||
+ | Shake Lagrangian Multipliers: | ||
+ | Rattle Lagrangian Multipliers: | ||
+ | Shake Lagrangian Multipliers: | ||
+ | Rattle Lagrangian Multipliers: | ||
+ | </ | ||
+ | |||
+ | <note warning> | ||
+ | Make sure that you get the units right. The Largange multipliers are written in atomic units (Hartree/ | ||
+ | </ | ||
+ | |||
+ | * From these files you can calculate the average Lagrange multiplier of the Shake-algorithm like this: | ||
+ | < | ||
+ | grep Shake yourprojectname.LagrangeMultLog | awk '{c++ ; s=s+$4}END{print s/c}' | ||
+ | </ | ||
+ | |||
+ | * The average Lagrange multiplier is the average force $F(x)$ required to constrain the atoms at the distance $x$. | ||
+ | * From these forces the free energy difference can be obtained via TI (see **Background**) | ||
+ | |||
+ | |||
+ | <note tip> | ||
+ | * Calculate $\Delta A$ numerically using the trapezoidal rule (or equivalent) with EXCEL, ORIGIN or any scripting language. | ||
+ | </ | ||
+ | |||
+ |
exercises/2017_uzh_acpc2/prot_fol.1495023195.txt.gz · Last modified: 2020/08/21 10:15 (external edit)