Copernicus
Getting Started
Prerequisites
Python
Network Ports
Git
Downloading Copernicus
Server Setup
Additional prerequisites
Installation
Optmizing the server
Client Setup
Logging in
Worker Setup
Prerequisites
Installation
Summary
Copernicus overlay network
Server
Where to run the server
Fault tolerance of projects
Creating a Copernicus network with many servers
Worker delegation
Connecting servers
Connecting to a server that is behind a firewall.
User management
Worker
Worker and Server communication
Automatic partitioning
Limiting the number of cores
Running jobs from a specific project
Avoiding idle workers
Specifying work directory
Platform types
Executing workers in a cluster environment
Best practices when using 1000+ cores
Tutorials
Introductory Tutorial
Installation
Creating a workflow for molecular simulations
Listing workflow functions
Providing input files to our project.
Looking at the results
Running more simulations.
Pausing a project
Finishing a project
MSM Tutorial
Prerequisites
Learning the method
Overview of the workflow
Settings
How to determine what parameters to set?
Example 1: Alanine dipeptide
Example 2: fs-peptide
Free Energy Tutorial
Prerequisites
Learning the method
Overview of the workflow
Settings
Solvation Free Energy
Binding Free Energy
How to determine what parameters to set?
Example 1: Hydration Free Energy of Ethanol
Example 2: Binding Free Energy of Ethanol to Ethanol
String-of-swarms method
Introduction
Prerequisites
Method protocol
Restrained minimization (run_minimization)
Restrained thermalization (thermalization)
Restrained equilibration (run_restrained)
Swarm preparation (prep_swarms)
Swarm (swarms)
CV extraction (get_cvs)
Reparametrization (reparametrize)
Demo running
Parameter reference
General settings
String specification
Minimization stage settings
Thermalization stage settings
Equilibration and Swarm stage settings
Developer Documentation
Submitting Pull requetsts
Writing Documentation
Copernicus
Docs
»
Tutorials
Edit on GitHub
Tutorials
ΒΆ
Contents:
Introductory Tutorial
Installation
Creating a workflow for molecular simulations
Listing workflow functions
Providing input files to our project.
Looking at the results
Running more simulations.
Pausing a project
Finishing a project
MSM Tutorial
Prerequisites
Learning the method
Overview of the workflow
Settings
How to determine what parameters to set?
Free Energy Tutorial
Prerequisites
Learning the method
Overview of the workflow
Settings
How to determine what parameters to set?
Example 1: Hydration Free Energy of Ethanol
Example 2: Binding Free Energy of Ethanol to Ethanol
String-of-swarms method
Introduction
Prerequisites
Method protocol
Demo running
Parameter reference