exercises:2018_uzh_acpc2:prot_fol
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exercises:2018_uzh_acpc2:prot_fol [2018/05/18 18:42] – [Task 3: Evaluate the free energy difference] gtocci | exercises:2018_uzh_acpc2:prot_fol [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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Download the files: {{ : | Download the files: {{ : | ||
- | in the directory | + | in the directory |
'' | '' | ||
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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 > | ||
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cp deca_ala/* $d/. | cp deca_ala/* $d/. | ||
cd $d | cd $d | ||
- | sed -e "s|18.36|${d}|" | + | sed -e "s|14.37|${d}|" |
cp2k.sopt -i d_${d}.inp -o d_${d}.out | cp2k.sopt -i d_${d}.inp -o d_${d}.out | ||
cd .. | cd .. | ||
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<note tip> | <note tip> | ||
* Be careful with the values chosen for the upper and lower bound of the constraints as the simulations might crash or the SHAKE algorithm for the computation of the constraints might not converge if the values of the constrained distances are unphysical. | * Be careful with the values chosen for the upper and lower bound of the constraints as the simulations might crash or the SHAKE algorithm for the computation of the constraints might not converge if the values of the constrained distances are unphysical. | ||
- | * We have set the number of step of each constrained MD to 200000. Try to increase this number if you want to achieve better statistics or to decrease it to get the results faster, at the expense of a converged free energy. | + | * We have set the number of steps of each constrained MD to 5000. Try to increase this number if you want to achieve better statistics or to decrease it to get the results faster, at the expense of a more converged free energy. |
</ | </ | ||
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- | * From these files you can calculate the average Lagrange multiplier of the Shake-algorithm like this: | + | * From these files you can calculate the average Lagrange multiplier of the Shake-algorithm |
< | < | ||
- | grep Shake yourprojectname.LagrangeMultLog | awk '{c++ ; s=s+$4}END{print s/c}' | + | grep Shake yourprojectname.LagrangeMultLog | awk '{c++ ; s=s+$4; sq=sq+$4*$4 }END{print s/c, sqrt(sq/c - s*s/ |
</ | </ | ||
- | * The average Lagrange multiplier is the average force $F(x)$ required to constrain the atoms at the distance $x$. | + | * The average Lagrange multiplier is the average force $F(x)$ required to constrain the atoms at the distance $x$. First of all, plot the force $F(x)$ with its standard error as a function of the collective variable to see if the simulation carried out so far is statistically relevant or the relative error is too large. |
- | * From these forces the free energy difference can be obtained via thermodynamic integration between the two states. Given that state $a$ and $b$ are the initial and the final values of the collective variable, extract the free energy difference from | + | * From the forces, the free energy difference can be obtained via thermodynamic integration between the two states. Given that state $a$ and $b$ are the initial and the final values of the collective variable, extract the free energy difference from |
\begin{equation} | \begin{equation} | ||
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<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. | ||
* 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