From 568374d8cbe5f8a975e05089d5517c260566bb07 Mon Sep 17 00:00:00 2001 From: Giovanni Bussi <giovanni.bussi@gmail.com> Date: Wed, 24 Jul 2019 12:53:30 +0200 Subject: [PATCH] fix --- user-doc/tutorials/aa-lugano-6b.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/user-doc/tutorials/aa-lugano-6b.txt b/user-doc/tutorials/aa-lugano-6b.txt index 6dcdf4cf9..119bb72db 100644 --- a/user-doc/tutorials/aa-lugano-6b.txt +++ b/user-doc/tutorials/aa-lugano-6b.txt @@ -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! -- GitLab