(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2010

AMBER ADVANCED WORKSHOP

TUTORIAL A5

The Nudged Elastic Band Approach to Finding the Lowest Energy
Pathway Between two States

By Christina Bergonzo, Carlos Simmerling & Ross Walker

Psi

Phi

 

Potential Energy Scan for Phi/Psi Rotation of Alanine Dipeptide.
Dots show path found by Nudged Elastic Band (NEB) method.
The surface was calculated by scanning the two angles and extracting the energy
represented by the amber force field.

This tutorial introduces the Nudged Elastic Band method for finding low energy pathways for transitions. This feature has been significantly updated in Amber v11 and as such you will require a copy of AMBER 11 to complete this tutorial. For details on how to obtain AMBER v11.0 please see the amber website. For details of the AMBER 11 NEB installation please see:

This tutorial will show you how to use a simulated annealing version of Nudged Elastic Band (NEB) to locate a low energy transition pathway for the Phi-Psi isomerization of alanine dipeptide. The use of simulated annealing means that it is not necessary to provide an initial guess at the pathway, merely the end points will do. Secondly using simulated annealing means that the algorithm will not remain trapped in the local minimum.

This tutorial consists of seven sections:

  1. section1.htm : Background

  2. section2.htm : Constructing the Pathway End Points

  3. section3.htm : Creating the NEB prmtop and inpcrd files

  4. section4.htm : Heating the System

  5. section5.htm : Simulated Annealing and Equilibration

  6. section6.htm : Slow Cooling

  7. section7.htm : Extracting the Final Pathway and Visualizing the Results

 

Proceed to section 1: Background