diff --git a/user-doc/tutorials/belfast-8.txt b/user-doc/tutorials/belfast-8.txt index e5f5c572ae6ca50df6a8d2d939a47dd3a3b074a3..e7550d8f6ae9e0ef1f12c3ca6cb7655e69eca110 100644 --- a/user-doc/tutorials/belfast-8.txt +++ b/user-doc/tutorials/belfast-8.txt @@ -1,6 +1,85 @@ /** \page belfast-8 Belfast tutorial: Replica exchange II and Multiple walkers +\section Aims + +The aim of this tutorial is to introduce the users to the use of Bias-Exchange Metadynamics. We will go through the writing of +the input files for BEMETA for a simple case of three alanines and we will use METAGUI to to analyse them. We will compare +the results of WT-BEMETA and STANDARD-BEMETA with four independent runs on the four Collective Variables. Finally we will +use a simplified version of BEMETA that is Multiple Walkers Metadynamics. + +\section belfast-1-lo Learning Outcomes + +Once this tutorial is completed students will: + +- Know how to run a Bias-Exchange simulation using PLUMED and GROMACS +- Know how to analyse the results of BEMETA with the help of METAGUI +- Know how to run a Multiple Walker simulation + +\section Resources + +The <a href="tutorial-resources/belfast-8.tar.gz" download="belfast-8.tar.gz"> tarball </a> for this project contains the following files: + +- trajectory-short.xyz : a (short) trajectory for a 16 residue protein in xyz format. All calculations with plumed driver use this trajectory. +- template.pdb : a single frame from the trajectory that can be used in conjuction with the \ref MOLINFO command + +\section Instructions + +\subsection bemeta Bias-Exchange Metadynamics + +In all variants of metadynamics the free-energy landscape of the system is reconstructed by gradually +filling the local minima with gaussian hills. The dimensionality of the landscape is equal to the +number of CVs which are biased, and typically a number of CVs smaller than three is employed. +The reason for this is that qualitatively, if the CVs are not correlated among them, the simulation time +required to fill the free-energy landscape grows exponentially with the number of CVs. +This limitation can be severe when studying complex transformations or reactions in which +more than say three relevant CVs can be identified. + +A possible technique to overcome this limitation is parallel-tempering metadynamics, \ref belfast-7. +A different solution is performing a bias-exchange simulation: +in this approach a relatively large number N of CVs is chosen to describe the possible transformations +of the system (e.g., to study the conformations of a peptide one may consider all the dihedral angles between amino acids). +Then, N metadynamics simulations (replicas) are run on the same system at the same temperature, biasing a different +CV in each replica. + +Normally, in these conditions, each bias profile would converge very slowly to the +equilibrium free-energy, due to hysteresis. Instead, in the bias-exchange approach every fixed number of steps +(say 10,000) an exchange is attempted between a randomly selected pair of replicas \f$ a \f$ and \f$ b \f$. +The probability to accept the exchange is given by a Metropolis rule: + +\f[ +\begin{eqnarray} +\min\left( 1, \exp \left[ \beta ( V_G^a(x^a,t)+V_G^b(x^b,t)-V_G^a(x^b,t)-V_G^b(x^a,t) ) \right] \right) +\end{eqnarray} +\f] + +where \f$ x^{a} \f$ and \f$ x^{b} \f$ are the coordinates of replicas \f$a \f$ and \f$ b \f$ +and \f$ V_{G}^{a(b)}\left(x,t\right) \f$ is the metadynamics potential acting on the replica \f$ a \f$( \f$ b \f$). +Each trajectory evolves through the high dimensional free energy landscape in the space of the CVs sequentially biased by +different metadynamics potentials acting on one CV at each time. +The results of the simulation are N one-dimensional projections of the free energy. + +In the following example, a bias-exchange simulation is performed on a Ala-Ala-Ala peptide (zwitterionic form, in vacuum with +\f$ \epsilon=80 \f$, force field amber03), using the four backbone dihedral angles as CVs. + +Four replicas of the system are employed, each one biased on a different CV, +thus four similar Plumed input files are prepared as follows: + +\verbatim + +\endverbatim + +The four replicas start from the same GROMACS topology file replicated four times: topol0.tpr, topol1.tpr, topol2.tpr, topol3.tpr. +Finally, GROMACS is launched as a parallel run on 4 cores, with one replica per core, with the command + +\verbatim +mpirun -np 4 mdrun -plumed plumed -multi 4 -replex 10000 +\endverbatim + +where -replex 10000 indicates that every 10000 molecular-dynamics steps +all replicas are randomly paired (e.g. 0-2 and 1-3) and exchanges are attempted +between each pair (as printed in the GROMACS *.log files). + */ link: @subpage belfast-8