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6 Sampling Configuration Space

6.1 Replica Exchange

The Replica Exchange Concept This tutorial covers how to setup, run and postprocess replica exchange simulations using multisander and Amber 10 or later.

By Dan Roe, Asim Okur, Carlos Simmerling and Ross Walker

6.2 Conformational equilibria of poly-proline pentamer

TOC image for steered MD tutorial This tutorial describes a couple of ways to assess conformational equilibria of a short polyproline peptide using so called steered molecular dynamics, and the famous replica-exchange protocol: html, pdf, polyproline-tutorial-files.tar.bz2 (Warning: 60Mb).

By V. Babin and C. Sagui

6.3 Using Accelerated Molecular Dynamics (aMD) to enhance sampling

aMD sampling toc image In this tutorial, we will learn how to use AMBER's implementation of aMD to enhance sampling. In this tutorial we focus on the steps necesary to prepare and run an aMD simulation. We use the work we published on the discovery of long lived conformational transformations in the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein. We follow the preparation of the files and give sme information about aMD reweighting.

By Romelia Salomon Ferrer, Levi Pierce, and Ross Walker

6.4 Adaptive Steered Molecular Dynamics

This tutorial provides detailed instructions on how to perform Adaptive Steered Molecular Dynamics (ASMD) simulations. Compared to Steered Molecular Dynamics, ASMD has been shown to converge much faster while reducing the computational cost. The tutorial calculates the Potential Mean Force of unfolding a small alpha-helical peptide using two different velocities.

By T. Dwight McGee Jr., Hailey Bureau, Caley Allen, and Rigoberto Hernandez

6.5 Conformational equilibria of methyl-alpha-L-iduronic acid in explicit water

conformational flooding toc image This tutorial illustrates the use of conformational "flooding" to setup a Hamiltonian replica exchange simulation of a small molecule in explicit solvent.

By V. Babin and C. Sagui

6.6 Nudged Elastic Band (NEB) simulations

free energy landscape This tutorial uses a feature that is only available with Amber v11. As such you need to have Amber 11 installed to run the calculations in this tutorial, if you are using Amber 9 or 10 then you should use the older NEB tutorial. In the nudged elastic band method, the path for a conformational change is approximated with a series of images of the molecule describing the path. Minimisation of the entire system, but with the end point structures fixed, provides a minimum energy path. In this tutorial we will use the NEB method to predict a pathway for a conformational change in alanine dipeptide.

By Christina Bergonzo, Carlos Simmerling, and Ross Walker

"How's that for maxed out?"

Last modified: Aug 27, 2021