Sampling Configuration Space
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
The unified “middle” thermostat scheme in AMBER for efficient configurational sampling (Advanced)
This tutorial introduces the "middle" thermostat scheme, which is a
unified framework for the development of efficient thermostatting
algorityms for configurational sampling for the canonical ensemble. By the Jian Liu research group.
Weighted Ensemble Methods using WESTPA
The WESTPA strategy focuses computing power on transitions rather than
stable states. These simulation are more efficient than standard simulations
in sampling rare events such as protein binding. By
Jeremy Leung and Darian Yang.
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
equilibria of poly-proline pentamer
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
polyproline-tutorial-files.tar.bz2 (Warning: 60Mb).
By V. Babin and C. Sagui.
Molecular Dynamics (aMD) to enhance sampling
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
equilibria of methyl-alpha-L-iduronic acid in explicit water
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.
Elastic Band (NEB) simulations
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