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SEEKR: Simulation-Enabled Estimation of Kinetic Rates

Introduction
------------

SEEKR (http://amarolab.ucsd.edu/seekr/) is a suite of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory.


Instructions
------------

SEEKR is designed to be run on Linux. Obtain SEEKR by cloning the Git repository on github

git clone https://github.com/lvotapka/seekr.git

Or, go to the URL https://github.com/lvotapka/seekr and click the "Clone or download" button and save to a place in your computer.

From there, open seekr/doc/manual.txt to get started.


Files
-----

This is a description of the folders in the base seekr/ directory.
doc/ - Find detailed information about the installation, usage, tutorials, and troubleshooting of SEEKR in this folder
test/ - Most of the tests in SEEKR are integrated directly into the scripts, but some tests are run externally, and are included in this directory.
tools/ - A number of non-essential scripts are included in this directory that may be useful for calculations, preparations, and analysis.
website/ - a full copy of the SEEKR website


Getting Help
------------

Need help? Check out the documentation at http://amarolab.ucsd.edu/seekr/ or that is located in seekr/doc/manual.txt

Also, you can make comments, submit issues, and talk to real people at the Github site: http://github.com/lvotapka/seekr