Question

calculate rate of metadynamics simulation using plumed

Answer 1

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
Evaluate the convergence of a metadynamics simulation
Assess the choice of the collective variables
Resources

The TARBALL for this project contains the following files:

diala.pdb: a PDB file for alanine dipeptide in vacuo
topol.tpr: a GROMACS run file to perform MD of alanine dipeptide
do_block_fes.py: a python script to perform error analysis
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.

Answer 2

Write the PLUMED input file to perform metadynamics simulationsCalculate the free energy from a metadynamics runCompute the error associated to the reconstructed free energyEvaluate the convergence of a metadynamics simulationAssess the choice of the collective variablesResource