Stretching Deca-alanine Tutorial

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University of Illinois at Urbana-Champaign
Beckman Institute for Advanced Science and Technology
Theoretical and Computational Biophysics Group
Computational Biophysics Workshop

Stretching Deca-alanine

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Sanghyun Park

Fatemeh Khalili

Johan Strumpfer

FEB 2012

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Introduction
Setup
IMD simulation
SMD simulation
Viewing SMD trajectories within VMD
Analysis of the SMD trajectory
- PMF calculation
Acknowledgements

tutorial-l@ks.uiuc.edu