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Martin Kurečka
Plumed AlphaFold
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568374d8
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Commit
568374d8
authored
5 years ago
by
Giovanni Bussi
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user-doc/tutorials/aa-lugano-6b.txt
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@@ -137,14 +137,14 @@ Below you can find reference results
\subsection lugano-6b-ex-4 Exercise 4: Standard affinity
Now use the weights that you computed in the previous exercise to
compute the
standard
affinity of the Mg to the phosphate. In order to do
compute the
absolute binding
affinity of the Mg to the phosphate. In order to do
so you should compute the relative probability of seeing the Mg bound to the phosphate
and in the bulk region.
and in the bulk region
and normalize to 1 mol/M concentration
.
For instance, if you define bulk the region between 1.5 and 2.5 angstrom, you should
multiply
the
For instance, if you define bulk the region between 1.5 and 2.5 angstrom, you should
divide
the
weight of the unbound state by a factor \f$ \frac{4\pi}{3}(2.5^3-1.5^3)/V_{mol} \f$
where \f$V_{mol}=1.66\f$ is the volume corresponding to the inverse of 1 mol/L concentration.
The absolute binding affinity is then defined as \f$-k_BT \log \frac{w_B}{w_U} \f$.
You should obtain a value of approximately 50.4 kj/mol
\warning The trajectory is too short (approx 20ns) to obtain converged results!
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