exercises:2017_uzh_acpc2:prot_fol
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exercises:2017_uzh_acpc2:prot_fol [2017/05/17 12:04] – vrybkin | exercises:2017_uzh_acpc2:prot_fol [2017/05/17 12:47] – [Task 3: Evaluate the free energy difference] vrybkin | ||
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- | **deca_ala.pdb** (protein data base) file contains the coordinates | + | '' |
- | **deca_ala.psf** (protein structure file) file contains connectivity data | + | '' |
- | **par_all27_prot_lipid.inp** contains the force field parameters | + | '' |
- | **md_1836.inp** is the CP2K input file | + | '' |
- | Open the **deca_ala.pdb** protein data bank format file with **vmd**. Create a new representation for the protein, e.g. of type **Ribbon** to observe the alpha-helix. | + | Open the '' |
{{ : | {{ : | ||
===== 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 '' | ||
+ | |||
+ | - 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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1