diff --git a/user-doc/figs/lugano-6b-ffdpUB.png b/user-doc/figs/lugano-6b-ffdpUB.png deleted file mode 100644 index 92c5e8800197baad4105927fb001685ff75a8ffa..0000000000000000000000000000000000000000 Binary files a/user-doc/figs/lugano-6b-ffdpUB.png and /dev/null differ diff --git a/user-doc/tutorials/aa-lugano-6b.txt b/user-doc/tutorials/aa-lugano-6b.txt index 329b2fae4d514100e07eafecec6ec227f7e93a2b..a5aa3cae2dcc7e20b1e77cf13e2dfb7fe1160802 100644 --- a/user-doc/tutorials/aa-lugano-6b.txt +++ b/user-doc/tutorials/aa-lugano-6b.txt @@ -15,7 +15,10 @@ Once this tutorial is completed students will \section lugano-6b-resources Resources -The reference trajectory and other files can be obtained at XXX +The reference trajectory and other files can be obtained at this path +\verbatim +https://github.com/plumed/lugano2019/raw/master/lugano-6b.tgz +\endverbatim This tutorial has been tested on v2.5 but it should also work with other versions of PLUMED. @@ -129,7 +132,7 @@ A possible way to do so you can use \ref UPDATE_IF to extract portions of trajectory such that the Mg is bound or unbound. Below you can find reference results -\image html lugano-6b-ffUB.png "Free energy as a function of coordination between Mg and water oxygens, both for Mg bound and unbound" +\image html lugano-6b-ffcnUB.png "Free energy as a function of coordination between Mg and water oxygens, both for Mg bound and unbound" \subsection lugano-6b-ex-4 Exercise 4: Standard affinity @@ -138,9 +141,9 @@ compute the standard 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. -TO COMPLETE. - -\subsection +For instance, if you define bulk the region between 1.5 and 2.5 angstrom, you should multiply 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. */