From 5806f307a8b9b21517ca40951a615d93560f55af Mon Sep 17 00:00:00 2001 From: Massimiliano Bonomi <massimiliano.bonomi@gmail.com> Date: Wed, 28 May 2014 14:28:57 +0100 Subject: [PATCH] add link to Max's Dropbox --- user-doc/tutorials/belfast-6.txt | 32 +++++++++++++++++++++++++++++++- 1 file changed, 31 insertions(+), 1 deletion(-) diff --git a/user-doc/tutorials/belfast-6.txt b/user-doc/tutorials/belfast-6.txt index bfd23d340..600c1463e 100644 --- a/user-doc/tutorials/belfast-6.txt +++ b/user-doc/tutorials/belfast-6.txt @@ -1,10 +1,40 @@ /** \page belfast-6 Belfast tutorial: Metadynamics +\section Aims + +The aim of this tutorial is to introduce the users to running a metadynamics calculation using plumed. We will set up +a simple calculation on alanine dipeptide in vacuum, analize the output, and calculate free energies +from the simulation. We will also learn how to spot issues related to a bad choice of collective variables +and how to run a well-tempered metadynamics simulation. + +\section belfast-6-lo Learning Outcomes + +Once this tutorial is completed students will: + +- Know how to run a metadynamics calculation using plumed +- Know how to analyse the output of the simulation +- Know how to restart a metadynamics calculation +- Know how to calculate free energies from a metadynamics calculation +- Know how to detect issues with the choice of the collective variables +- Know how to run a well-tempered metadynamics calculation using plumed + +\section Resources + +The <a href="https://dl.dropboxusercontent.com/u/23916760/belfast-6.tar.gz" download="belfast-6.tar.gz"> tarball </a> for this project contains the following directories: + +- TOPO: it contains the gromacs topology and configuration files to simulate the alanine dipeptide in vacuum +- Exercise_1_2: plumed.dat is the input file to run a metadynamics simulation with 2 CVs +- Exercise_3: plumed.dat is the input file to restart a metadynamics simulation +- Exercise_4: analize_FES.sh is a bash script to calculate the free-energy difference between two basins as a function of simulation time +- Exercise_5: plumed.dat is the input file to run a metadynamics simulation with 1 CV +- Exercise_6: plumed.dat is the input file to run a well-tempered metadynamics simulation with 2 CVs + +\section Instructions + */ link: @subpage belfast-6 description: How to run a metadynamics simulation - -- GitLab