Welcome to RepEx’s documentation!

Contents:

• 1. Introduction
  • 1.1. What is RepEx ?
  • 1.2. What can I do with it?
  • 1.3. Why should I use it?
• 2. Installation
• 3. Getting Started
  • 3.1. Invoking RepEx
    • 3.1.1. Resource configuration file
    • 3.1.2. REMD input file for Amber kernel
• 4. User guide
  • 4.1. T-REMD example (peptide ala10) with Amber kernel
    • 4.1.1. Run locally
    • 4.1.2. Verify output
  • 4.2. US-REMD example using Alanine Dipeptide system with Amber kernel
    • 4.2.1. Run locally
    • 4.2.2. Verify output
  • 4.3. TUU-REMD example (alanine dipeptide) with Amber kernel
    • 4.3.1. Run locally
    • 4.3.2. Verify output
• 5. Running on HPC clusters
  • 5.1. T-REMD example (peptide ala10) with Amber kernel
    • 5.1.1. Verify output
  • 5.2. US-REMD example using Alanine Dipeptide system with Amber kernel
  • 5.3. TUU-REMD example (alanine dipeptide) with Amber kernel
• 6. Preview
  • 6.1. Replica Exchange Patterns
    • 6.1.1. Synchronous Replica Exchange Pattern
    • 6.1.2. Asynchronous Replica Exchange Pattern
  • 6.2. Flexible execution modes
    • 6.2.1. Execution Mode S1
    • 6.2.2. Execution Mode S2
    • 6.2.3. Execution Mode S3
• 7. Frequently Asked Questions
  • 7.1. Where are .mdout files?
  • 7.2. Where are .mdinfo files?
  • 7.3. How can I obtain information about accepted exchanges?

Indices and tables

• Index
• Module Index
• Search Page