From be5cee6b1addcc611261d1afd8d929e89c7f3ee9 Mon Sep 17 00:00:00 2001 From: Massimiliano Bonomi <massimiliano.bonomi@gmail.com> Date: Wed, 28 May 2014 14:39:18 +0100 Subject: [PATCH] change description of example 6 --- user-doc/tutorials/belfast-6.txt | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/user-doc/tutorials/belfast-6.txt b/user-doc/tutorials/belfast-6.txt index 600c1463e..a9b1885ca 100644 --- a/user-doc/tutorials/belfast-6.txt +++ b/user-doc/tutorials/belfast-6.txt @@ -5,8 +5,8 @@ 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. +from the simulation. We will also learn how to run a well-tempered metadynamics simulation and +detect issues related to a bad choice of collective variables. \section belfast-6-lo Learning Outcomes @@ -16,19 +16,19 @@ Once this tutorial is completed students will: - 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 run a well-tempered metadynamics calculation using plumed - 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 +- Exercise_1_2: run a metadynamics simulation with 2 CVs, dihedral phi and psi +- Exercise_3: restart a metadynamics simulation +- Exercise_4: calculate free energies from a metadynamics simulation and monitor the convergence +- Exercise_5: run a well-tempered metadynamics simulation with 2 CVs, dihedral phi and psi +- Exercise_6: run a well-tempered metadynamics simulation with 1 CV, dihedral psi \section Instructions -- GitLab