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repex 0.2 documentation
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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
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Index
Module Index
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Table Of Contents
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