(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 2015

AMBER ADVANCED TUTORIALS
TUTORIAL A2

A Coupled Potential QM/MM Simulation

By Ross Walker

Updated for AMBER 15

With the version 9 release of AMBER came the ability to do fast and accurate coupled potential semi-empirical QM/MM simulations with full treatment of long range electrostatics (PME) or Generalized Born implicit solvent simulations. This tutorial uses the theory described in section 10 of the AMBER 15 manual in which one part of the system can be represented quantum mechanically while the rest of the system is represented using the classical AMBER force field.

This tutorial explains how to set up a periodic boundary QM/MM simulation using AMBER. Currently the QM/MM functionality of AMBER is implemented within the standard sander executable.

This tutorial consists of 4 sections:

  1. section1.htm : Setting up NMA

  2. section2.htm : Classical MD

  3. section3.htm : QM/MM MD

  4. section4.htm : Comparing the results


CLICK HERE TO GO TO SECTION 1


(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 2015