diff --git a/user-doc/figs/lugano-6b-ffcn.png b/user-doc/figs/lugano-6b-ffcn.png index 563111f9feab419dc088ecf818ee1e813a5cf38e..9b57adf7e88692358e72c4139273e974de373008 100644 Binary files a/user-doc/figs/lugano-6b-ffcn.png and b/user-doc/figs/lugano-6b-ffcn.png differ diff --git a/user-doc/figs/lugano-6b-ffdc.png b/user-doc/figs/lugano-6b-ffdc.png index c6a7ffbc4fe4885c9389c133234bdfed2d809414..d60913d628534d6b10651121b5ee352429dd8e61 100644 Binary files a/user-doc/figs/lugano-6b-ffdc.png and b/user-doc/figs/lugano-6b-ffdc.png differ diff --git a/user-doc/figs/lugano-6b-ffdnUB.png b/user-doc/figs/lugano-6b-ffdnUB.png index 441dcf204c631afb257eb528d5a79be880655514..42095270c4ed1e73dd3557cd7ada2fe6fd745d09 100644 Binary files a/user-doc/figs/lugano-6b-ffdnUB.png and b/user-doc/figs/lugano-6b-ffdnUB.png differ diff --git a/user-doc/figs/lugano-6b-ffdp.png b/user-doc/figs/lugano-6b-ffdp.png index b592240f3f7c508434de8d066e633c01ee12f4a6..40603d46f8c88a3e6bd46832f1c5ce62f37a956e 100644 Binary files a/user-doc/figs/lugano-6b-ffdp.png and b/user-doc/figs/lugano-6b-ffdp.png differ diff --git a/user-doc/figs/lugano-6b-ffdpUB.png b/user-doc/figs/lugano-6b-ffdpUB.png index 8c90a02379c62a60cb35b04eac5281f81d6b3e09..92c5e8800197baad4105927fb001685ff75a8ffa 100644 Binary files a/user-doc/figs/lugano-6b-ffdpUB.png and b/user-doc/figs/lugano-6b-ffdpUB.png differ diff --git a/user-doc/tutorials/aa-lugano-6b.txt b/user-doc/tutorials/aa-lugano-6b.txt index ae877c455ac760e295784f17baae5de2c7471156..329b2fae4d514100e07eafecec6ec227f7e93a2b 100644 --- a/user-doc/tutorials/aa-lugano-6b.txt +++ b/user-doc/tutorials/aa-lugano-6b.txt @@ -15,10 +15,7 @@ Once this tutorial is completed students will \section lugano-6b-resources Resources -The \tarball{lugano-6b} for this project contains the following files: - -- xx: -- xx: +The reference trajectory and other files can be obtained at XXX This tutorial has been tested on v2.5 but it should also work with other versions of PLUMED. @@ -32,10 +29,14 @@ no internal degree of freedom, and instead of a protein with a complex binding p We are also assuming to know which is the proper binding site, since we can easily guess that the most stable binding will happen on the phosphate. -Since running these simulations on your laptop would take too long, you will be able to download -all the output files for a decently long simulation at this PATH. +Since running these simulations on your laptop would take too long, you will start +with the output files obtained with a decently long simulation and analyse them. + +\warning The trajectory is too short (approx 20ns) to obtain converged results! +To get real numbers, please run it longer. -Before continuing, please read carefully the `plumed.dat` file since there you will find all the explanations +Before continuing, please read carefully the `plumed.dat` file that was used to produce the +simulation, since there you will find all the explanations about which variables were biased and how. In case you want to do analysis with python, you can use the included `plumed_pandas.py` module, @@ -61,6 +62,17 @@ It works in this way: As the title says, just compute the free-energy landscape as a function of the biased collective variable (namely, distance between the Mg ion and the phosphate and coordination number of the Mg ion with water oxygens). +You should just use \ref sum_hills with the usual options. In order to visualize the result with gnuplot +you might use something like this: + +\verbatim +gnuplot> set pm3d map +gnuplot> p "fes.dat" u 1:2:3 +\endverbatim + +You should obtain a plot similar to this one: + +\image html lugano-6b-fes.png "Free energy as a function of distance from phosphate and coordination with water" \subsection lugano-6b-ex-2 Exercise 2: Visualizing the trajectory @@ -98,10 +110,26 @@ The free energy as a function of the distance between Mg and geometric center of be used to identify the bulk region. In order to do so, normalize it adding the correct entropic term \f$ k_BT \log d^2 \f$, and find a region where the free energy is approximately constant to represent the bulk region. +You can for instance use the following commands in gnuplot +\verbatim +gnuplot> p "fes_dc" u 1:2 , "" u 1:($2+2.5*log($1) +\endverbatim +Below you can find reference results + +\image html lugano-6b-ffdp.png "Free energy as a function of distance between Mg and phosphate" +\image html lugano-6b-ffdc.png "Free energy as a function of distance between Mg and RNA center" +\image html lugano-6b-ffcn.png "Free energy as a function of coordination between Mg and water oxygens" + +Also try to compute conditional free energies: - coordination number between Mg and water _assuming Mg is bound to phosphate_. - coordination number between Mg and water _assuming Mg is in the bulk_. +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" \subsection lugano-6b-ex-4 Exercise 4: Standard affinity