diff --git a/user-doc/figs/trieste-6-bard1.png b/user-doc/figs/trieste-6-bard1.png new file mode 100644 index 0000000000000000000000000000000000000000..611e6a09be10b04b54878b124f94b06123837998 Binary files /dev/null and b/user-doc/figs/trieste-6-bard1.png differ diff --git a/user-doc/tutorials/a-trieste-4.txt b/user-doc/tutorials/a-trieste-4.txt index 886362f1bb841be259be5fd6a4387f4017e54fd4..68a11799ca7826bb79363d4b90f19bd4a3c33fb7 100644 --- a/user-doc/tutorials/a-trieste-4.txt +++ b/user-doc/tutorials/a-trieste-4.txt @@ -10,7 +10,6 @@ of the collective variables used, and estimating the associated error. \section trieste-4-objectives Objectives Once this tutorial is completed students will be able to: - - Write the PLUMED input file to perform metadynamics simulations - Calculate the free energy from a metadynamics run - Compute the error associated to the reconstructed free energy diff --git a/user-doc/tutorials/a-trieste-6.txt b/user-doc/tutorials/a-trieste-6.txt new file mode 100644 index 0000000000000000000000000000000000000000..5795508feaef9bbfba68fa66555fe058b0c68ada --- /dev/null +++ b/user-doc/tutorials/a-trieste-6.txt @@ -0,0 +1,82 @@ +/** +\page trieste-6 Trieste tutorial: Real-life applications with complex CVs + +\section trieste-6-aims Aims + +The aim of this tutorial is to train users to +learn the syntax of complex collective variables and use them to analyze +MD trajectories of realistic biological systems and bias them with metadynamics. + +\section trieste-6-objectives Objectives + +Once this tutorial is completed students will be able to: +- Write the PLUMED input file to use complex CVs for analysis +- Analyze trajectories and calculate the free energy of complex biological systems +- Perform error analysis and evaluate convergence in realistic situations +- Setup, run, and analyze metadynamics simulations of a complex system + +\section trieste-6-resources Resources + +The reference trajectories and input files for the exercizes proposed in this tutorial +can be downloaded from `github` using the following command: + +\verbatim +wget +\endverbatim + +This tutorial has been tested on a pre-release version of version 2.4. However, it should not take advantage +of 2.4-only features, thus should also work with version 2.3. + +\section trieste-6-intro Introduction + +In this tutorial we propose exercizes on the following biological systems: +- the BRCA1-associated RING domain protein 1 (BARD1 complex) +- the cmyc peptide in presence of urea at low concentration (cmyc-UREA) +- xxxx + +\section trieste-6-ex-1 Exercize 1: analyzing trajectory of the BARD1 complex + +The BARD1 complex is a heterodimer composed by two domains of 112 and 117 residues each. +The sytem is represented at coarse-grained level using the MARTINI force field. + +\anchor trieste-6-bard1 +\image html trieste-6-bard1.png "The BARD1 heterodimer" + +In the TARBALL of this exercize, we provide a long MD simulation of the BARD1 complex in which +the two domains explore multiple different conformations. + +The users are expected to: +- calculate the values of different CVs on the trajectory +- estimate the free energies as a function of the CVs tested (mono- and multi-dimensional) +- extracting from the trajectories the configurations corresponding to relevant free-energy minima +- calculate the error in the associated free energy using the block analysis technique +- evaluate the convergence of the original trajectory + +The user is free to choose his/her favorite CVs. +However, we encourage all the users to experiments at least with the following CVs. + +1) RMSD from the native state + + +2) Distance from the native contact map + + +3) A CV describing the relative orientation of the two chains. + + +\section trieste-6-conclusions Conclusions + +In summary, in this tutorial you should have learned how to use PLUMED to: +- Setup and run a metadynamics calculation. +- Compute free energies from the metadynamics bias potential using the \ref sum_hills utility. +- Calculate the error in the reconstructed free energy using block analysis. +- Discriminate between good and bad collective variables. +- Evaluate the convergence of a metadynamics simulation. + +*/ + +link: @subpage trieste-6 + +description: This tutorial explains how to use PLUMED to run metadynamics simulations + +additional-files: trieste-6