3.4 Alternate script for initial relaxation

This is a short introduction to relaxation protocols described here:

D.R. Roe and B.R. Brooks. A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations. J. Chem. Phys. 153:054123, 2020. PDF version.

Learning Outcomes

• Explore "modern" ideas for relaxation (sometime called equilibration) for molecular dynamics systems, especially for "difficult" systems.

Overview

This is not really a tutorial, per se. It is rather an attempt to point users to the paper listed above, and to provide links to Amber-compatible scripts that implement that protocol.

The paper by Roe and Brooks describes a somewhat complex, but heavily tested set of steps to relax starting structures (which might have a number of internal problems) to "stable" systems that are suitable for further exploration by molecular dynamics. Note that "relaxed" does not mean "equilibrated" (which rarely occurs for more than rather simple systems.)

What to do next:

• Read the paper cited above. You don't need to read every sentence, but you do need to follow the logic to understand why various steps are taken, what might go wrong, and how to avoid pitfalls.
• Got to Dan Roe's AmberMdPrep page, and try out the scripts there: this is an Amber-specific implementation of the ideas in the J. Chem. Phys. paper.