Shape-Based Coarse Graining

Next: Introduction

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

Shape-Based Coarse Graining

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Anton Arkhipov

Ying Yin

Danielle Chandler

Jen Hsin

Kirby Vandivort

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Introduction
Required Programs
Getting Started
Coarse-graining an atomic structure
- Coarse-graining of a BAR domain monomer.
  - SBCG Builder output files.
- Mapping the coarse-grained monomer structure onto a different copy of the monomer.
Parameterizing SBCG force field
Building a shape-based coarse-grained membrane
- Generate a patch of coarse-grained membrane.
- Add charged lipids to the membrane patch.
Combining proteins and membrane for a simulation
Running a coarse-grained simulation
- Preparing a configuration file.
- Simulation outputs.

tutorial-l@ks.uiuc.edu